rs164911

Variant names:

• chr1-91085255-G-T
• rs164911

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 0.17 in 152,016 control chromosomes in the GnomAD database, including 3,504 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 0.17 (3504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25796 AN: 151898 Hom.: 3497 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.170 AC: 25824 AN: 152016 Hom.: 3504 Cov.: 32 AF XY: 0.166 AC XY: 12363 AN XY: 74312

African (AFR) AF: 0.384 AC: 15878 AN: 41396

American (AMR) AF: 0.101 AC: 1539 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.150 AC: 775 AN: 5156

South Asian (SAS) AF: 0.0293 AC: 141 AN: 4810

European-Finnish (FIN) AF: 0.101 AC: 1074 AN: 10582

Middle Eastern (MID) AF: 0.114 AC: 33 AN: 290

European-Non Finnish (NFE) AF: 0.0825 AC: 5608 AN: 68014

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.121 Hom.: 3638

Bravo AF: 0.180

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs164911; hg19: chr1-91550812;