rs699947

Variant names:

• chr6-43768652-A-C
• rs699947

Your query was ambiguous. Multiple possible variants found:

• chr6-43768652-A-C
• chr6-43768652-A-T

GermlineCancer (beta)

Variant summary

Our verdict is

Benign

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

. The variant received -13 classification points (ACMG Germline Pathogenicity v2019): 0P and 13B. BA1BP4_StrongBP6

The variant 6-43768652-A-C has been identified. The variant allele was found at a cumulative frequency of 0.597 (AC=90,880) in the gnomAD database across 152,102 control chromosomes, including 28,280 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.782. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Variant has been reported in ClinVar as Benign/Likely Benign (no review stars).

• Frequency: Genomes: 𝑓 0.60 (28280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 1.03
• Publications: 797 publications found

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -13 points.

• BP4: Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
• BP6: ClinVar 0-star benign — supporting (BP6); ClinVar germline classification: Benign/Likely Benign, 0 star(s).
• BA1: GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.7816 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90793 AN: 151984 Hom.: 28251 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.597 AC: 90880 AN: 152102 Hom.: 28280 Cov.: 33 AF XY: 0.595 AC XY: 44239 AN XY: 74346

African (AFR) AF: 0.789 AC: 32720 AN: 41482

American (AMR) AF: 0.613 AC: 9374 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3727 AN: 5152

South Asian (SAS) AF: 0.552 AC: 2665 AN: 4824

European-Finnish (FIN) AF: 0.447 AC: 4727 AN: 10578

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34085 AN: 67980

Other (OTH) AF: 0.616 AC: 1302 AN: 2112

Alfa AF: 0.549 Hom.: 14592

Bravo AF: 0.623

Asia WGS AF: 0.611 AC: 2124 AN: 3478

Local populations

ToMMo 61KJPN (+60KJPN MNV) AF: 0.688 AC: 84336 AN: 122664

Turkish Variome AF: 0.579 AC: 895 AN: 1546 Hom.: 265

WBBC (Westlake BioBank for Chinese) pilot AF: 0.736 AC: 6591 AN: 8960 Hom.: 2428

ABraOM SABE-WGS-1171 AF: 0.629 AC: 1472 AN: 2342 Hom.: 487

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	Atherosclerosis, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.75
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs699947;

hg19: chr6-43736389;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar