rs6919798

Variant names:

• chr6-32765113-A-G
• rs6919798

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 0.0593 in 152,222 control chromosomes in the GnomAD database, including 345 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 0.059 (345 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 8 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 (AMR) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

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: 0.0593 AC: 9024 AN: 152104 Hom.: 344 Cov.: 31

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.00622

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.0593 AC: 9026 AN: 152222 Hom.: 345 Cov.: 31 AF XY: 0.0557 AC XY: 4146 AN XY: 74424

African (AFR) AF: 0.0672 AC: 2792 AN: 41522

American (AMR) AF: 0.0887 AC: 1357 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3466

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5176

South Asian (SAS) AF: 0.00623 AC: 30 AN: 4818

European-Finnish (FIN) AF: 0.00528 AC: 56 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4352 AN: 68014

Other (OTH) AF: 0.0872 AC: 184 AN: 2110

Alfa AF: 0.0633 Hom.: 285

Bravo AF: 0.0696

Asia WGS AF: 0.0120 AC: 42 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	7.9
DANN	Benign	0.82
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs6919798; hg19: chr6-32732890;