rs2788935

Variant names:

• chr6-132542225-T-C
• rs2788935

Your query was ambiguous. Multiple possible variants found:

• chr6-132542225-T-C
• chr6-132542225-T-G

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 0.312 in 151,350 control chromosomes in the GnomAD database, including 7,540 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 0.31 (7540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 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: 0.312 AC: 47210 AN: 151230 Hom.: 7539 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.312 AC: 47244 AN: 151350 Hom.: 7540 Cov.: 32 AF XY: 0.311 AC XY: 23012 AN XY: 73984

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.301

Alfa AF: 0.306 Hom.: 884

Bravo AF: 0.307

Asia WGS AF: 0.179 AC: 621 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2788935; hg19: chr6-132863364; COSMIC: COSV71512312;