1-4506671-T-C

Position:

• chr1-4506671-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;