8-75571621-C-T

Variant names:

• chr8-75571621-C-T
• rs1399564

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 0.663 in 152,026 control chromosomes in the GnomAD database, including 34,812 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 0.66 (34812 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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: 0.663 AC: 100734 AN: 151908 Hom.: 34779 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.663 AC: 100818 AN: 152026 Hom.: 34812 Cov.: 31 AF XY: 0.661 AC XY: 49146 AN XY: 74310

African (AFR) AF: 0.838 AC: 34783 AN: 41492

American (AMR) AF: 0.494 AC: 7555 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1944 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2057 AN: 5144

South Asian (SAS) AF: 0.549 AC: 2648 AN: 4822

European-Finnish (FIN) AF: 0.729 AC: 7693 AN: 10548

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.618 AC: 42001 AN: 67958

Other (OTH) AF: 0.640 AC: 1352 AN: 2114

Alfa AF: 0.599 Hom.: 9334

Bravo AF: 0.649

Asia WGS AF: 0.495 AC: 1720 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	0.070
DANN	Benign	0.79
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1399564; hg19: chr8-76483856;