chr6-30964532-C-T

Variant names:

• chr6-30964532-C-T
• rs2844697

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;