rs6940344

Positions:

• chr6-2914375-A-C

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 0.484 in 151,954 control chromosomes in the GnomAD database, including 20,417 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 0.48 (20417 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73440 AN: 151836 Hom.: 20377 Cov.: 31

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.484 AC: 73546 AN: 151954 Hom.: 20417 Cov.: 31 AF XY: 0.476 AC XY: 35328 AN XY: 74230

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.434

Alfa AF: 0.396 Hom.: 12193

Bravo AF: 0.485

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6940344; hg19: chr6-2914609;