rs871913

Variant names:

• chr20-16163700-G-A
• rs871913

Your query was ambiguous. Multiple possible variants found:

• chr20-16163700-G-A
• chr20-16163700-G-C
• chr20-16163700-G-T

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 0.13 in 152,090 control chromosomes in the GnomAD database, including 1,594 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 0.13 (1594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.175 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: 0.130 AC: 19781 AN: 151970 Hom.: 1595 Cov.: 32

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.130 AC: 19783 AN: 152090 Hom.: 1594 Cov.: 32 AF XY: 0.130 AC XY: 9680 AN XY: 74350

African (AFR) AF: 0.0351 AC: 1456 AN: 41520

American (AMR) AF: 0.140 AC: 2138 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3470

East Asian (EAS) AF: 0.0687 AC: 356 AN: 5182

South Asian (SAS) AF: 0.125 AC: 600 AN: 4792

European-Finnish (FIN) AF: 0.200 AC: 2111 AN: 10558

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12097 AN: 67982

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.153 Hom.: 3275

Bravo AF: 0.122

Asia WGS AF: 0.115 AC: 397 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	3.7
DANN	Benign	0.47
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs871913; hg19: chr20-16144345;