7-99802509-A-T

Variant names:

• chr7-99802509-A-T
• rs12705060

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 0.476 in 151,906 control chromosomes in the GnomAD database, including 19,976 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 0.48 (19976 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72269 AN: 151788 Hom.: 19975 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.476 AC: 72281 AN: 151906 Hom.: 19976 Cov.: 31 AF XY: 0.481 AC XY: 35713 AN XY: 74268

African (AFR) AF: 0.172 AC: 7109 AN: 41404

American (AMR) AF: 0.594 AC: 9070 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2050 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3547 AN: 5166

South Asian (SAS) AF: 0.572 AC: 2754 AN: 4812

European-Finnish (FIN) AF: 0.571 AC: 6032 AN: 10558

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39928 AN: 67912

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.491 Hom.: 2345

Bravo AF: 0.465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.27
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs12705060; hg19: chr7-99400132;