1-152569753-T-C

Variant names:

• chr1-152569753-T-C
• rs7516108

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 0.645 in 151,678 control chromosomes in the GnomAD database, including 31,997 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 0.64 (31997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97729 AN: 151560 Hom.: 31949 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.645 AC: 97823 AN: 151678 Hom.: 31997 Cov.: 32 AF XY: 0.648 AC XY: 48022 AN XY: 74140

African (AFR) AF: 0.722 AC: 29863 AN: 41364

American (AMR) AF: 0.618 AC: 9315 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1926 AN: 3464

East Asian (EAS) AF: 0.562 AC: 2905 AN: 5166

South Asian (SAS) AF: 0.613 AC: 2948 AN: 4812

European-Finnish (FIN) AF: 0.701 AC: 7406 AN: 10562

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41542 AN: 67914

Other (OTH) AF: 0.597 AC: 1258 AN: 2106

Alfa AF: 0.608 Hom.: 43273

Bravo AF: 0.642

Asia WGS AF: 0.592 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7516108; hg19: chr1-152542229;