rs7750826

chr6-1336632-A-Gchr6-1336632-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.246 in 152,162 control chromosomes in the GnomAD database, including 4,956 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 0.25 (4956 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37346 AN: 152044 Hom.: 4951 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.246 AC: 37370 AN: 152162 Hom.: 4956 Cov.: 33 AF XY: 0.254 AC XY: 18885 AN XY: 74370

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.223

Alfa AF: 0.243 Hom.: 9576

Bravo AF: 0.244

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	6.0
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7750826; hg19: chr6-1336867;