7-1245559-A-T

Variant names:

• chr7-1245559-A-T
• rs10277115

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 0.577 in 152,138 control chromosomes in the GnomAD database, including 29,550 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 0.58 (29550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• Publications: 31 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 (NFE) allele frequency at 95% confidence interval = 0.755 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: 0.577 AC: 87754 AN: 152020 Hom.: 29551 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.577 AC: 87765 AN: 152138 Hom.: 29550 Cov.: 32 AF XY: 0.577 AC XY: 42947 AN XY: 74368

African (AFR) AF: 0.226 AC: 9385 AN: 41512

American (AMR) AF: 0.592 AC: 9048 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2581 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5170

South Asian (SAS) AF: 0.680 AC: 3283 AN: 4826

European-Finnish (FIN) AF: 0.758 AC: 8023 AN: 10584

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51689 AN: 67978

Other (OTH) AF: 0.591 AC: 1250 AN: 2116

Alfa AF: 0.574 Hom.: 2162

Bravo AF: 0.546

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.12
DANN	Benign	0.52
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs10277115; hg19: chr7-1285195;