rs7745308

Positions:

• chr6-132573289-T-G

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 0.0624 in 152,178 control chromosomes in the GnomAD database, including 565 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 0.062 (565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

ACMG classification

Verdict is Benign. Variant got -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 = 0.152 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: 0.0624 AC: 9481 AN: 152060 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0624 AC: 9495 AN: 152178 Hom.: 565 Cov.: 32 AF XY: 0.0602 AC XY: 4482 AN XY: 74406

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0280

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0433 Hom.: 59

Bravo AF: 0.0693

Asia WGS AF: 0.0180 AC: 61 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	3.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7745308; hg19: chr6-132894428;