rs4959119

Positions:

• chr6-32877952-T-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 0.353 in 151,998 control chromosomes in the GnomAD database, including 9,648 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 0.35 (9648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 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: 0.353 AC: 53674 AN: 151880 Hom.: 9638 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.353 AC: 53715 AN: 151998 Hom.: 9648 Cov.: 31 AF XY: 0.347 AC XY: 25802 AN XY: 74310

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.369

Alfa AF: 0.362 Hom.: 1606

Bravo AF: 0.361

Asia WGS AF: 0.319 AC: 1110 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959119; hg19: chr6-32845729; COSMIC: COSV105346472;