rs31966

Variant names:

• chr16-22709045-G-A
• rs31966

Your query was ambiguous. Multiple possible variants found:

• chr16-22709045-G-A
• chr16-22709045-G-C
• chr16-22709045-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 0.429 in 152,060 control chromosomes in the GnomAD database, including 17,696 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 0.43 (17696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.21
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 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: 0.430 AC: 65264 AN: 151942 Hom.: 17700 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.429 AC: 65241 AN: 152060 Hom.: 17696 Cov.: 32 AF XY: 0.423 AC XY: 31421 AN XY: 74334

African (AFR) AF: 0.123 AC: 5104 AN: 41498

American (AMR) AF: 0.398 AC: 6074 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3472

East Asian (EAS) AF: 0.153 AC: 790 AN: 5170

South Asian (SAS) AF: 0.349 AC: 1683 AN: 4820

European-Finnish (FIN) AF: 0.578 AC: 6094 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41811 AN: 67960

Other (OTH) AF: 0.457 AC: 964 AN: 2110

Alfa AF: 0.498 Hom.: 10085

Bravo AF: 0.401

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.93
PhyloP100		-6.2

Splicing

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

Other links and lift over

dbSNP: rs31966; hg19: chr16-22720366;