7-51868999-T-C

Variant names:

• chr7-51868999-T-C
• rs665087

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 0.563 in 152,094 control chromosomes in the GnomAD database, including 25,652 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 0.56 (25652 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.563 AC: 85581 AN: 151974 Hom.: 25606 Cov.: 33

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.563 AC: 85679 AN: 152094 Hom.: 25652 Cov.: 33 AF XY: 0.571 AC XY: 42448 AN XY: 74372

African (AFR) AF: 0.714 AC: 29623 AN: 41486

American (AMR) AF: 0.628 AC: 9594 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1885 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4875 AN: 5178

South Asian (SAS) AF: 0.614 AC: 2964 AN: 4826

European-Finnish (FIN) AF: 0.503 AC: 5312 AN: 10560

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29672 AN: 67972

Other (OTH) AF: 0.542 AC: 1144 AN: 2112

Alfa AF: 0.481 Hom.: 14741

Bravo AF: 0.580

Asia WGS AF: 0.739 AC: 2562 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.65
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs665087; hg19: chr7-51936695;