7-15609310-T-C

Variant names:

• chr7-15609310-T-C
• rs11525793

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 0.0508 in 152,154 control chromosomes in the GnomAD database, including 642 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 0.051 (642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 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: 0.0507 AC: 7705 AN: 152036 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.0738

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.0372

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00496

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0508 AC: 7730 AN: 152154 Hom.: 642 Cov.: 32 AF XY: 0.0557 AC XY: 4147 AN XY: 74392

African (AFR) AF: 0.0738 AC: 3063 AN: 41514

American (AMR) AF: 0.0994 AC: 1518 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.387 AC: 1990 AN: 5148

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4830

European-Finnish (FIN) AF: 0.0502 AC: 532 AN: 10592

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00496 AC: 337 AN: 68004

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0182 Hom.: 239

Bravo AF: 0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.74
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11525793; hg19: chr7-15648935;