8-61954382-A-T

Variant names:

• chr8-61954382-A-T
• rs344287

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 0.721 in 151,820 control chromosomes in the GnomAD database, including 40,709 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 0.72 (40709 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 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: 0.721 AC: 109435 AN: 151702 Hom.: 40665 Cov.: 31

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.721 AC: 109531 AN: 151820 Hom.: 40709 Cov.: 31 AF XY: 0.715 AC XY: 53011 AN XY: 74124

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.712

Alfa AF: 0.685 Hom.: 4523

Bravo AF: 0.731

Asia WGS AF: 0.739 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344287; hg19: chr8-62866941;