rs788173

Variant names:

• chr2-172088732-G-A
• rs788173
• NM_178120.5:c.*475G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-172088732-G-A
• chr2-172088732-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178120.5(DLX1):​c.*475G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,954 control chromosomes in the GnomAD database, including 14,988 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.41 (14912 hom., cov: 34)
  • Exomes 𝑓: 0.35 (76 hom.)
• Consequence: DLX1 NM_178120.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 13 publications found

Genes affected

DLX1 (HGNC:2914): (distal-less homeobox 1) This gene encodes a member of a homeobox transcription factor gene family similiar to the Drosophila distal-less gene. The encoded protein is localized to the nucleus where it may function as a transcriptional regulator of signals from multiple TGF-{beta} superfamily members. The encoded protein may play a role in the control of craniofacial patterning and the differentiation and survival of inhibitory neurons in the forebrain. This gene is located in a tail-to-tail configuration with another member of the family on the long arm of chromosome 2. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ENSG00000288958 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178120.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX1	NM_178120.5	MANE Select	c.*475G>A		3_prime_UTR	Exon 3 of 3	NP_835221.2
	DLX1	NM_001038493.2		c.*653G>A		3_prime_UTR	Exon 2 of 2	NP_001033582.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DLX1	ENST00000361725.5	TSL:1 MANE Select	c.*475G>A		3_prime_UTR	Exon 3 of 3	ENSP00000354478.4
	DLX1	ENST00000341900.6	TSL:1	c.*653G>A		3_prime_UTR	Exon 2 of 2	ENSP00000341786.6
	DLX1	ENST00000475989.2	TSL:2	n.1317G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62892 AN: 151738 Hom.: 14890 Cov.: 34

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.354 AC: 389 AN: 1098 Hom.: 76 Cov.: 0 AF XY: 0.332 AC XY: 215 AN XY: 648

African (AFR) AF: 0.719 AC: 23 AN: 32

American (AMR) AF: 0.583 AC: 7 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 13 AN: 30

East Asian (EAS) AF: 0.286 AC: 4 AN: 14

South Asian (SAS) AF: 0.375 AC: 3 AN: 8

European-Finnish (FIN) AF: 0.358 AC: 157 AN: 438

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.325 AC: 164 AN: 504

Other (OTH) AF: 0.310 AC: 18 AN: 58

GnomAD4 genome AF: 0.415 AC: 62960 AN: 151856 Hom.: 14912 Cov.: 34 AF XY: 0.409 AC XY: 30363 AN XY: 74242

African (AFR) AF: 0.659 AC: 27245 AN: 41330

American (AMR) AF: 0.314 AC: 4795 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5184

South Asian (SAS) AF: 0.302 AC: 1457 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3685 AN: 10540

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22058 AN: 67924

Other (OTH) AF: 0.403 AC: 849 AN: 2106

Alfa AF: 0.346 Hom.: 11242

Bravo AF: 0.425

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs788173; hg19: chr2-172953460; COSMIC: COSV59394350; COSMIC: COSV59394350;