rs4285401

Variant names:

• chr7-153181248-A-G
• rs4285401

Variant summary

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

The variant allele was found at a frequency of 0.413 in 151,972 control chromosomes in the GnomAD database, including 15,296 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 (15296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62782 AN: 151854 Hom.: 15298 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.413 AC: 62771 AN: 151972 Hom.: 15296 Cov.: 32 AF XY: 0.407 AC XY: 30240 AN XY: 74276

African (AFR) AF: 0.156 AC: 6473 AN: 41456

American (AMR) AF: 0.400 AC: 6108 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1919 AN: 3466

East Asian (EAS) AF: 0.236 AC: 1218 AN: 5164

South Asian (SAS) AF: 0.466 AC: 2241 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5253 AN: 10560

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38031 AN: 67934

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.507 Hom.: 70783

Bravo AF: 0.390

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.63
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4285401; hg19: chr7-152878333;