rs2844619

Positions:

• chr6-31274446-C-G
• chr6-31274446-C-T

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 0.66 in 150,490 control chromosomes in the GnomAD database, including 32,728 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 0.66 (32728 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.660 AC: 99189 AN: 150378 Hom.: 32710 Cov.: 27

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.660 AC: 99249 AN: 150490 Hom.: 32728 Cov.: 27 AF XY: 0.665 AC XY: 48869 AN XY: 73522

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.693

Alfa AF: 0.363 Hom.: 433

Bravo AF: 0.657

Asia WGS AF: 0.744 AC: 2591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844619; hg19: chr6-31242223;