rs2844724

Positions:

• chr6-30501413-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 0.693 in 152,076 control chromosomes in the GnomAD database, including 36,719 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 0.69 (36719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

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 (AFR) allele frequency at 95% confidence interval = 0.763 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: 0.693 AC: 105338 AN: 151958 Hom.: 36679 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.693 AC: 105425 AN: 152076 Hom.: 36719 Cov.: 32 AF XY: 0.691 AC XY: 51341 AN XY: 74324

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.687

Alfa AF: 0.666 Hom.: 18783

Bravo AF: 0.693

Asia WGS AF: 0.678 AC: 2361 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	0.69
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844724; hg19: chr6-30469190;