chr6-160846303-A-G

Variant names:

• chr6-160846303-A-G
• rs9355841

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 0.613 in 151,776 control chromosomes in the GnomAD database, including 28,952 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 0.61 (28952 hom., cov: 30)
• Consequence: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 10 publications found

Genes affected

LOC107986665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92875 AN: 151658 Hom.: 28900 Cov.: 30

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.613 AC: 92987 AN: 151776 Hom.: 28952 Cov.: 30 AF XY: 0.619 AC XY: 45927 AN XY: 74158

African (AFR) AF: 0.618 AC: 25580 AN: 41378

American (AMR) AF: 0.704 AC: 10735 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1818 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5050 AN: 5158

South Asian (SAS) AF: 0.741 AC: 3568 AN: 4812

European-Finnish (FIN) AF: 0.556 AC: 5855 AN: 10526

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.566 AC: 38405 AN: 67884

Other (OTH) AF: 0.638 AC: 1344 AN: 2106

Alfa AF: 0.586 Hom.: 78032

Bravo AF: 0.622

Asia WGS AF: 0.842 AC: 2923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.2
DANN	Benign	0.28
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs9355841; hg19: chr6-161267335;