rs1382606

chr8-97569988-G-Achr8-97569988-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.641 in 152,052 control chromosomes in the GnomAD database, including 33,724 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 0.64 (33724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.641 AC: 97321 AN: 151934 Hom.: 33658 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.641 AC: 97451 AN: 152052 Hom.: 33724 Cov.: 32 AF XY: 0.639 AC XY: 47454 AN XY: 74304

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.648

Alfa AF: 0.538 Hom.: 30387

Bravo AF: 0.677

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	14
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1382606; hg19: chr8-98582216;