chr8-34379474-C-T

Variant names:

• chr8-34379474-C-T
• rs2609653

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 0.943 in 152,240 control chromosomes in the GnomAD database, including 67,675 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 0.94 (67675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.965 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: 0.943 AC: 143406 AN: 152122 Hom.: 67621 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.943 AC: 143518 AN: 152240 Hom.: 67675 Cov.: 32 AF XY: 0.941 AC XY: 70009 AN XY: 74424

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.951

Alfa AF: 0.949 Hom.: 111949

Bravo AF: 0.946

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2609653; hg19: chr8-34236992;