rs1396977

Variant names:

• chr8-130710456-T-A
• rs1396977

Your query was ambiguous. Multiple possible variants found:

• chr8-130710456-T-A
• chr8-130710456-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 0.42 in 151,938 control chromosomes in the GnomAD database, including 13,515 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 0.42 (13515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

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 (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.420 AC: 63732 AN: 151820 Hom.: 13494 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.420 AC: 63809 AN: 151938 Hom.: 13515 Cov.: 32 AF XY: 0.417 AC XY: 30968 AN XY: 74258

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.386

Alfa AF: 0.391 Hom.: 1448

Bravo AF: 0.422

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1396977; hg19: chr8-131722702;