7-46211934-T-C

Variant names:

• chr7-46211934-T-C
• rs2054789

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 0.465 in 152,164 control chromosomes in the GnomAD database, including 18,588 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 0.46 (18588 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 4 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 = 0.654 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: 0.465 AC: 70711 AN: 152046 Hom.: 18589 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.465 AC: 70715 AN: 152164 Hom.: 18588 Cov.: 33 AF XY: 0.472 AC XY: 35148 AN XY: 74398

African (AFR) AF: 0.202 AC: 8389 AN: 41518

American (AMR) AF: 0.534 AC: 8159 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3481 AN: 5172

South Asian (SAS) AF: 0.525 AC: 2533 AN: 4826

European-Finnish (FIN) AF: 0.585 AC: 6197 AN: 10598

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37948 AN: 67978

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

Alfa AF: 0.492 Hom.: 2612

Bravo AF: 0.449

Asia WGS AF: 0.568 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.64
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2054789; hg19: chr7-46251532;