chr6-159164909-A-G

Variant names:

• chr6-159164909-A-G
• rs295340

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 0.53 in 152,080 control chromosomes in the GnomAD database, including 21,571 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 0.53 (21571 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80469 AN: 151962 Hom.: 21549 Cov.: 33

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.530 AC: 80536 AN: 152080 Hom.: 21571 Cov.: 33 AF XY: 0.531 AC XY: 39484 AN XY: 74322

African (AFR) AF: 0.537 AC: 22284 AN: 41462

American (AMR) AF: 0.614 AC: 9391 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1696 AN: 3472

East Asian (EAS) AF: 0.618 AC: 3196 AN: 5174

South Asian (SAS) AF: 0.558 AC: 2694 AN: 4824

European-Finnish (FIN) AF: 0.491 AC: 5199 AN: 10582

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34356 AN: 67974

Other (OTH) AF: 0.542 AC: 1140 AN: 2102

Alfa AF: 0.514 Hom.: 78728

Bravo AF: 0.542

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.071
DANN	Benign	0.26
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs295340; hg19: chr6-159585941; COSMIC: COSV51946470;