7-51868999-T-C

Variant names:

• chr7-51868999-T-C
• rs665087

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.542

Alfa AF: 0.477 Hom.: 12189

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665087; hg19: chr7-51936695;