6-141254229-C-T

Variant names:

• chr6-141254229-C-T
• rs967794

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 0.0895 in 152,058 control chromosomes in the GnomAD database, including 986 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 0.090 (986 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 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: 0.0894 AC: 13588 AN: 151940 Hom.: 982 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.0895 AC: 13610 AN: 152058 Hom.: 986 Cov.: 31 AF XY: 0.0910 AC XY: 6768 AN XY: 74340

African (AFR) AF: 0.177 AC: 7354 AN: 41450

American (AMR) AF: 0.0502 AC: 768 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3468

East Asian (EAS) AF: 0.178 AC: 917 AN: 5148

South Asian (SAS) AF: 0.185 AC: 894 AN: 4822

European-Finnish (FIN) AF: 0.0335 AC: 354 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2578 AN: 67996

Other (OTH) AF: 0.0982 AC: 207 AN: 2108

Alfa AF: 0.0659 Hom.: 78

Bravo AF: 0.0917

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs967794; hg19: chr6-141575366;