1-4506671-T-C

Variant names:

• chr1-4506671-T-C
• rs7537577

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.581 in 151,992 control chromosomes in the GnomAD database, including 25,930 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 0.58 (25930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.581 AC: 88198 AN: 151874 Hom.: 25903 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.581 AC: 88275 AN: 151992 Hom.: 25930 Cov.: 32 AF XY: 0.583 AC XY: 43311 AN XY: 74294

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.612

Alfa AF: 0.551 Hom.: 4741

Bravo AF: 0.597

Asia WGS AF: 0.683 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7537577; hg19: chr1-4566731; COSMIC: COSV59919787;