6-132576719-G-A

Position:

• chr6-132576719-G-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 0.753 in 152,170 control chromosomes in the GnomAD database, including 43,570 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 0.75 (43570 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114504 AN: 152052 Hom.: 43520 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.753 AC: 114613 AN: 152170 Hom.: 43570 Cov.: 33 AF XY: 0.757 AC XY: 56297 AN XY: 74398

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.725

Alfa AF: 0.723 Hom.: 56641

Bravo AF: 0.746

Asia WGS AF: 0.694 AC: 2411 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7765655; hg19: chr6-132897858;