1-104563876-T-C

Variant names:

• chr1-104563876-T-C
• rs7553985

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 0.369 in 151,798 control chromosomes in the GnomAD database, including 10,777 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 0.37 (10777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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: 0.369 AC: 55944 AN: 151682 Hom.: 10767 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.369 AC: 56002 AN: 151798 Hom.: 10777 Cov.: 32 AF XY: 0.371 AC XY: 27547 AN XY: 74156

African (AFR) AF: 0.298 AC: 12368 AN: 41448

American (AMR) AF: 0.400 AC: 6082 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1231 AN: 3462

East Asian (EAS) AF: 0.618 AC: 3180 AN: 5142

South Asian (SAS) AF: 0.514 AC: 2472 AN: 4808

European-Finnish (FIN) AF: 0.291 AC: 3081 AN: 10574

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.388 AC: 26289 AN: 67830

Other (OTH) AF: 0.396 AC: 835 AN: 2108

Alfa AF: 0.386 Hom.: 6416

Bravo AF: 0.371

Asia WGS AF: 0.503 AC: 1748 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	3.2
DANN	Benign	0.68
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs7553985; hg19: chr1-105106498;