8-34379474-C-T

Variant names:

• chr8-34379474-C-T
• rs2609653

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.938 AC: 38957 AN: 41536

American (AMR) AF: 0.939 AC: 14351 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3446 AN: 3470

East Asian (EAS) AF: 0.956 AC: 4949 AN: 5176

South Asian (SAS) AF: 0.988 AC: 4764 AN: 4820

European-Finnish (FIN) AF: 0.902 AC: 9564 AN: 10606

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64279 AN: 68030

Other (OTH) AF: 0.951 AC: 2013 AN: 2116

Alfa AF: 0.948 Hom.: 178642

Bravo AF: 0.946

Asia WGS AF: 0.968 AC: 3367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.63
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2609653; hg19: chr8-34236992;