rs295340

Positions:

• chr6-159164909-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.542

Alfa AF: 0.510 Hom.: 33573

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

Splicing

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

Publications

LitVar

Other links and lift over

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