rs2844697

chr6-30964532-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 0.425 in 148,740 control chromosomes in the GnomAD database, including 15,255 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 0.42 (15255 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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: 0.425 AC: 63136 AN: 148626 Hom.: 15239 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.425 AC: 63202 AN: 148740 Hom.: 15255 Cov.: 31 AF XY: 0.412 AC XY: 30010 AN XY: 72780

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.407

Alfa AF: 0.354 Hom.: 16729

Bravo AF: 0.433

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.084
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844697; hg19: chr6-30932309;