7-52100392-C-T

Variant names:

• chr7-52100392-C-T
• rs2464946

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 0.631 in 152,004 control chromosomes in the GnomAD database, including 31,170 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 0.63 (31170 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.721 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: 0.631 AC: 95915 AN: 151886 Hom.: 31148 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.631 AC: 95986 AN: 152004 Hom.: 31170 Cov.: 33 AF XY: 0.625 AC XY: 46454 AN XY: 74314

African (AFR) AF: 0.477 AC: 19749 AN: 41412

American (AMR) AF: 0.673 AC: 10292 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2317 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2499 AN: 5150

South Asian (SAS) AF: 0.630 AC: 3040 AN: 4822

European-Finnish (FIN) AF: 0.613 AC: 6487 AN: 10588

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.726 AC: 49361 AN: 67960

Other (OTH) AF: 0.648 AC: 1367 AN: 2110

Alfa AF: 0.704 Hom.: 59941

Bravo AF: 0.628

Asia WGS AF: 0.587 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2464946; hg19: chr7-52168088;