rs2840836

chr6-132558216-A-Gchr6-132558216-A-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 0.796 in 152,108 control chromosomes in the GnomAD database, including 48,654 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 0.80 (48654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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: 0.796 AC: 120985 AN: 151990 Hom.: 48619 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.796 AC: 121076 AN: 152108 Hom.: 48654 Cov.: 32 AF XY: 0.798 AC XY: 59276 AN XY: 74326

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.796

Alfa AF: 0.776 Hom.: 5689

Bravo AF: 0.799

Asia WGS AF: 0.864 AC: 3005 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2840836; hg19: chr6-132879355; COSMIC: COSV51587164;