7-150815084-T-C

Variant names:

• chr7-150815084-T-C
• rs10231759

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 0.411 in 151,998 control chromosomes in the GnomAD database, including 14,468 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 0.41 (14468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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: 0.411 AC: 62383 AN: 151880 Hom.: 14436 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.411 AC: 62458 AN: 151998 Hom.: 14468 Cov.: 32 AF XY: 0.416 AC XY: 30922 AN XY: 74306

African (AFR) AF: 0.591 AC: 24470 AN: 41392

American (AMR) AF: 0.388 AC: 5929 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3702 AN: 5172

South Asian (SAS) AF: 0.530 AC: 2552 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3735 AN: 10580

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19639 AN: 67972

Other (OTH) AF: 0.384 AC: 809 AN: 2108

Alfa AF: 0.334 Hom.: 22235

Bravo AF: 0.424

Asia WGS AF: 0.588 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.61
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10231759; hg19: chr7-150512172;