rs140174

Variant names:

• chr22-23580796-A-G
• rs140174
• XM_011530206.2:c.*806T>C

Variant summary

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

The ENST00000608615.1(ENSG00000272733):​n.*84T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 153,562 control chromosomes in the GnomAD database, including 19,445 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 0.45 (19349 hom., cov: 32)
  • Exomes 𝑓: 0.35 (96 hom.)
• Consequence: ENSG00000272733 ENST00000608615.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 18 publications found

Genes affected

DRICH1 (HGNC:28031): (aspartate rich 1)

ENSG00000272733 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608615.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272733	ENST00000608615.1	TSL:3	n.*84T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68365 AN: 151962 Hom.: 19297 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.349 AC: 516 AN: 1480 Hom.: 96 AF XY: 0.344 AC XY: 269 AN XY: 782

African (AFR) AF: 0.688 AC: 11 AN: 16

American (AMR) AF: 0.473 AC: 191 AN: 404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.808 AC: 21 AN: 26

South Asian (SAS) AF: 0.526 AC: 40 AN: 76

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.258 AC: 231 AN: 896

Other (OTH) AF: 0.352 AC: 19 AN: 54

GnomAD4 genome AF: 0.450 AC: 68478 AN: 152082 Hom.: 19349 Cov.: 32 AF XY: 0.451 AC XY: 33562 AN XY: 74342

African (AFR) AF: 0.762 AC: 31614 AN: 41484

American (AMR) AF: 0.433 AC: 6609 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4101 AN: 5156

South Asian (SAS) AF: 0.473 AC: 2273 AN: 4808

European-Finnish (FIN) AF: 0.219 AC: 2323 AN: 10602

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18818 AN: 67970

Other (OTH) AF: 0.443 AC: 934 AN: 2110

Alfa AF: 0.342 Hom.: 40850

Bravo AF: 0.482

Asia WGS AF: 0.660 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-0.73
PromoterAI		-0.019	Neutral

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs140174;

hg19: chr22-23922983;