6-103245460-C-T

Variant names:

• chr6-103245460-C-T
• rs1547024

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 0.607 in 151,876 control chromosomes in the GnomAD database, including 30,006 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 0.61 (30006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 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: 0.606 AC: 92023 AN: 151758 Hom.: 29951 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.607 AC: 92129 AN: 151876 Hom.: 30006 Cov.: 31 AF XY: 0.597 AC XY: 44312 AN XY: 74208

African (AFR) AF: 0.854 AC: 35407 AN: 41452

American (AMR) AF: 0.467 AC: 7116 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1754 AN: 5148

South Asian (SAS) AF: 0.411 AC: 1976 AN: 4812

European-Finnish (FIN) AF: 0.494 AC: 5190 AN: 10500

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36631 AN: 67936

Other (OTH) AF: 0.599 AC: 1263 AN: 2108

Alfa AF: 0.576 Hom.: 3267

Bravo AF: 0.619

Asia WGS AF: 0.425 AC: 1477 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs1547024; hg19: chr6-103693335;