8-5750141-T-C

Variant names:

• chr8-5750141-T-C
• rs1707420

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 0.558 in 151,942 control chromosomes in the GnomAD database, including 24,221 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 0.56 (24221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.558 AC: 84702 AN: 151824 Hom.: 24202 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.558 AC: 84770 AN: 151942 Hom.: 24221 Cov.: 32 AF XY: 0.560 AC XY: 41587 AN XY: 74234

African (AFR) AF: 0.588 AC: 24367 AN: 41458

American (AMR) AF: 0.632 AC: 9643 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2094 AN: 3468

East Asian (EAS) AF: 0.889 AC: 4582 AN: 5156

South Asian (SAS) AF: 0.599 AC: 2886 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5052 AN: 10538

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34384 AN: 67928

Other (OTH) AF: 0.552 AC: 1163 AN: 2108

Alfa AF: 0.531 Hom.: 87845

Bravo AF: 0.570

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1707420; hg19: chr8-5607663;