1-163588959-T-C

Variant names:

• chr1-163588959-T-C
• rs10917804

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 0.0858 in 152,210 control chromosomes in the GnomAD database, including 640 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 0.086 (640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 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: 0.0858 AC: 13049 AN: 152092 Hom.: 642 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.0858 AC: 13057 AN: 152210 Hom.: 640 Cov.: 32 AF XY: 0.0854 AC XY: 6354 AN XY: 74434

African (AFR) AF: 0.0808 AC: 3354 AN: 41534

American (AMR) AF: 0.111 AC: 1693 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1154 AN: 5172

South Asian (SAS) AF: 0.108 AC: 520 AN: 4814

European-Finnish (FIN) AF: 0.0630 AC: 669 AN: 10616

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5063 AN: 67998

Other (OTH) AF: 0.0898 AC: 190 AN: 2116

Alfa AF: 0.0792 Hom.: 1952

Bravo AF: 0.0915

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs10917804; hg19: chr1-163558749;