chr6-83783631-G-C

Variant names:

• chr6-83783631-G-C
• rs6454338

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 0.582 in 152,060 control chromosomes in the GnomAD database, including 30,839 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 0.58 (30839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88415 AN: 151942 Hom.: 30841 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.582 AC: 88427 AN: 152060 Hom.: 30839 Cov.: 32 AF XY: 0.585 AC XY: 43509 AN XY: 74334

African (AFR) AF: 0.194 AC: 8055 AN: 41488

American (AMR) AF: 0.543 AC: 8293 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2528 AN: 3466

East Asian (EAS) AF: 0.482 AC: 2478 AN: 5144

South Asian (SAS) AF: 0.685 AC: 3305 AN: 4824

European-Finnish (FIN) AF: 0.849 AC: 8980 AN: 10574

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52589 AN: 67978

Other (OTH) AF: 0.587 AC: 1240 AN: 2114

Alfa AF: 0.675 Hom.: 4764

Bravo AF: 0.540

Asia WGS AF: 0.564 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.47
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6454338; hg19: chr6-84493350; COSMIC: COSV64076862;