rs34229995

chr6-15243787-C-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 0.0203 in 152,258 control chromosomes in the GnomAD database, including 61 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 0.020 (61 hom., cov: 32)
  • Exomes 𝑓: 0.056 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAdExome4 highest population allele frequency = 0.0556 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: 0.0203 AC: 3088 AN: 152122 Hom.: 61 Cov.: 32

Gnomad AFR AF: 0.00355

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.00982

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.0556 AC: 1 AN: 18 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.0203 AC: 3087 AN: 152240 Hom.: 61 Cov.: 32 AF XY: 0.0227 AC XY: 1689 AN XY: 74430

Gnomad4 AFR AF: 0.00354

Gnomad4 AMR AF: 0.00981

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0267 Hom.: 4

Bravo AF: 0.0143

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
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: rs34229995; hg19: chr6-15244018;