rs6564958

Variant names:

• chr16-82017510-G-A
• rs6564958

Your query was ambiguous. Multiple possible variants found:

• chr16-82017510-G-A
• chr16-82017510-G-C
• chr16-82017510-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 0.379 in 149,544 control chromosomes in the GnomAD database, including 11,508 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 0.38 (11508 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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: 0.379 AC: 56603 AN: 149444 Hom.: 11485 Cov.: 27

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.379 AC: 56653 AN: 149544 Hom.: 11508 Cov.: 27 AF XY: 0.372 AC XY: 27091 AN XY: 72890

African (AFR) AF: 0.529 AC: 21273 AN: 40214

American (AMR) AF: 0.282 AC: 4241 AN: 15018

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1431 AN: 3448

East Asian (EAS) AF: 0.294 AC: 1499 AN: 5098

South Asian (SAS) AF: 0.405 AC: 1918 AN: 4734

European-Finnish (FIN) AF: 0.269 AC: 2716 AN: 10092

Middle Eastern (MID) AF: 0.455 AC: 131 AN: 288

European-Non Finnish (NFE) AF: 0.332 AC: 22485 AN: 67666

Other (OTH) AF: 0.363 AC: 756 AN: 2082

Alfa AF: 0.337 Hom.: 14560

Bravo AF: 0.382

Asia WGS AF: 0.343 AC: 1194 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	0.71
DANN	Benign	0.33
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6564958; hg19: chr16-82051115;