4-111781479-A-G

Variant names:

• chr4-111781479-A-G
• rs1585471
• ENST00000751011.1:n.125+21161T>C

Variant summary

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

The ENST00000751011.1(ENSG00000297804):​n.125+21161T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,024 control chromosomes in the GnomAD database, including 7,354 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 0.31 (7354 hom., cov: 32)
• Consequence: ENSG00000297804 ENST00000751011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 15 publications found

Genes affected

ENSG00000297804 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297804	ENST00000751011.1	n.125+21161T>C		intron_variant	Intron 1 of 3
ENSG00000297804	ENST00000751012.1	n.89+21161T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46873 AN: 151908 Hom.: 7348 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.295

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.308 AC: 46886 AN: 152024 Hom.: 7354 Cov.: 32 AF XY: 0.310 AC XY: 23073 AN XY: 74332

African (AFR) AF: 0.293 AC: 12143 AN: 41452

American (AMR) AF: 0.342 AC: 5226 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2377 AN: 5164

South Asian (SAS) AF: 0.459 AC: 2208 AN: 4810

European-Finnish (FIN) AF: 0.241 AC: 2552 AN: 10590

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20506 AN: 67944

Other (OTH) AF: 0.292 AC: 617 AN: 2112

Alfa AF: 0.313 Hom.: 15666

Bravo AF: 0.312

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.80
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1585471; hg19: chr4-112702635;