6-129729465-T-C

Variant names:

• chr6-129729465-T-C
• rs7753327

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 0.356 in 152,022 control chromosomes in the GnomAD database, including 10,020 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 0.36 (10020 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.356 AC: 54010 AN: 151904 Hom.: 10006 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.356 AC: 54058 AN: 152022 Hom.: 10020 Cov.: 31 AF XY: 0.357 AC XY: 26510 AN XY: 74306

African (AFR) AF: 0.276 AC: 11462 AN: 41478

American (AMR) AF: 0.401 AC: 6130 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5166

South Asian (SAS) AF: 0.477 AC: 2291 AN: 4804

European-Finnish (FIN) AF: 0.379 AC: 4006 AN: 10560

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26354 AN: 67944

Other (OTH) AF: 0.372 AC: 787 AN: 2116

Alfa AF: 0.378 Hom.: 48938

Bravo AF: 0.351

Asia WGS AF: 0.405 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.32
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs7753327; hg19: chr6-130050610;