chr8-42693096-C-T

Variant names:

• chr8-42693096-C-T
• rs1530847

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 0.77 in 152,066 control chromosomes in the GnomAD database, including 45,880 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 0.77 (45880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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: 0.770 AC: 116997 AN: 151946 Hom.: 45850 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.770 AC: 117084 AN: 152066 Hom.: 45880 Cov.: 31 AF XY: 0.773 AC XY: 57484 AN XY: 74340

African (AFR) AF: 0.616 AC: 25535 AN: 41432

American (AMR) AF: 0.780 AC: 11911 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2847 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4170 AN: 5166

South Asian (SAS) AF: 0.798 AC: 3839 AN: 4808

European-Finnish (FIN) AF: 0.846 AC: 8961 AN: 10594

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57125 AN: 68006

Other (OTH) AF: 0.774 AC: 1631 AN: 2108

Alfa AF: 0.817 Hom.: 193815

Bravo AF: 0.756

Asia WGS AF: 0.765 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.26
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1530847; hg19: chr8-42548239;