7-152690784-T-G

Variant names:

• chr7-152690784-T-G
• rs10234749

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.837 AC: 34708 AN: 41478

American (AMR) AF: 0.736 AC: 11182 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3065 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3187 AN: 5168

South Asian (SAS) AF: 0.794 AC: 3827 AN: 4818

European-Finnish (FIN) AF: 0.659 AC: 6956 AN: 10554

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52920 AN: 67964

Other (OTH) AF: 0.809 AC: 1704 AN: 2106

Alfa AF: 0.777 Hom.: 67249

Bravo AF: 0.787

Asia WGS AF: 0.731 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.59
DANN	Benign	0.37
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs10234749; hg19: chr7-152387869;