6-131896547-C-T

Variant names:

• chr6-131896547-C-T
• rs7753048

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 0.173 in 148,126 control chromosomes in the GnomAD database, including 2,706 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 0.17 (2706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.172 AC: 25513 AN: 148026 Hom.: 2696 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.173 AC: 25565 AN: 148126 Hom.: 2706 Cov.: 32 AF XY: 0.178 AC XY: 12798 AN XY: 71986

African (AFR) AF: 0.293 AC: 11844 AN: 40422

American (AMR) AF: 0.143 AC: 2103 AN: 14754

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 376 AN: 3438

East Asian (EAS) AF: 0.136 AC: 657 AN: 4814

South Asian (SAS) AF: 0.171 AC: 776 AN: 4538

European-Finnish (FIN) AF: 0.201 AC: 1937 AN: 9644

Middle Eastern (MID) AF: 0.147 AC: 40 AN: 272

European-Non Finnish (NFE) AF: 0.110 AC: 7367 AN: 67264

Other (OTH) AF: 0.152 AC: 314 AN: 2072

Alfa AF: 0.120 Hom.: 2877

Bravo AF: 0.168

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.37
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7753048; hg19: chr6-132217687;