rs9355841

Variant names:

• chr6-160846303-A-G
• rs9355841

Your query was ambiguous. Multiple possible variants found:

• chr6-160846303-A-G
• chr6-160846303-A-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 0.613 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986665		n.160846303A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;