7-52213737-T-C

Variant names:

• chr7-52213737-T-C
• rs6592988

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 0.854 in 152,196 control chromosomes in the GnomAD database, including 55,533 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 0.85 (55533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.88
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.888 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: 0.854 AC: 129813 AN: 152078 Hom.: 55494 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.854 AC: 129905 AN: 152196 Hom.: 55533 Cov.: 33 AF XY: 0.856 AC XY: 63735 AN XY: 74420

African (AFR) AF: 0.836 AC: 34697 AN: 41502

American (AMR) AF: 0.901 AC: 13774 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4420 AN: 5162

South Asian (SAS) AF: 0.848 AC: 4090 AN: 4824

European-Finnish (FIN) AF: 0.911 AC: 9650 AN: 10598

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57378 AN: 68022

Other (OTH) AF: 0.854 AC: 1807 AN: 2116

Alfa AF: 0.857 Hom.: 8661

Bravo AF: 0.852

Asia WGS AF: 0.836 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.091
DANN	Benign	0.37
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs6592988; hg19: chr7-52281433;