7-152690784-T-G

Position:

• chr7-152690784-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 0.78 in 151,960 control chromosomes in the GnomAD database, including 46,520 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 0.78 (46520 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.780 AC: 118400 AN: 151840 Hom.: 46478 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.780 AC: 118501 AN: 151960 Hom.: 46520 Cov.: 31 AF XY: 0.772 AC XY: 57346 AN XY: 74264

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.809

Alfa AF: 0.758 Hom.: 6536

Bravo AF: 0.787

Asia WGS AF: 0.731 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.59
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10234749; hg19: chr7-152387869;