7-51888193-C-T

Variant names:

• chr7-51888193-C-T
• rs7785376

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 0.816 in 152,154 control chromosomes in the GnomAD database, including 51,025 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 0.82 (51025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.816 AC: 124118 AN: 152036 Hom.: 50974 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.816 AC: 124225 AN: 152154 Hom.: 51025 Cov.: 32 AF XY: 0.820 AC XY: 60965 AN XY: 74384

African (AFR) AF: 0.893 AC: 37057 AN: 41520

American (AMR) AF: 0.837 AC: 12801 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2546 AN: 3472

East Asian (EAS) AF: 0.959 AC: 4962 AN: 5172

South Asian (SAS) AF: 0.815 AC: 3929 AN: 4818

European-Finnish (FIN) AF: 0.821 AC: 8685 AN: 10578

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51769 AN: 67990

Other (OTH) AF: 0.799 AC: 1687 AN: 2112

Alfa AF: 0.774 Hom.: 35328

Bravo AF: 0.823

Asia WGS AF: 0.881 AC: 3064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.45
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7785376; hg19: chr7-51955889;