rs7774158

chr6-33039975-C-A

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 0.318 in 151,964 control chromosomes in the GnomAD database, including 8,352 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 0.32 (8352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.318 AC: 48284 AN: 151844 Hom.: 8345 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.318 AC: 48308 AN: 151964 Hom.: 8352 Cov.: 32 AF XY: 0.326 AC XY: 24205 AN XY: 74280

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.331

Alfa AF: 0.361 Hom.: 15450

Bravo AF: 0.298

Asia WGS AF: 0.437 AC: 1517 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	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7774158; hg19: chr6-33007752;