rs705993

Positions:

• chr8-69239440-C-T

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 0.672 in 152,068 control chromosomes in the GnomAD database, including 35,500 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 0.67 (35500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102095 AN: 151950 Hom.: 35491 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.672 AC: 102147 AN: 152068 Hom.: 35500 Cov.: 32 AF XY: 0.668 AC XY: 49670 AN XY: 74328

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.718

Alfa AF: 0.706 Hom.: 4799

Bravo AF: 0.670

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs705993; hg19: chr8-70151675;