7-135755167-A-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 0.739 in 152,162 control chromosomes in the GnomAD database, including 42,323 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 0.74 (42323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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: 0.739 AC: 112365 AN: 152044 Hom.: 42249 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.739 AC: 112498 AN: 152162 Hom.: 42323 Cov.: 32 AF XY: 0.741 AC XY: 55146 AN XY: 74390

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.737

Alfa AF: 0.670 Hom.: 68308

Bravo AF: 0.748

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10257539; hg19: chr7-135439915;