rs7991424

Variant names:

• chr13-45659190-G-A
• rs7991424

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 0.0542 in 152,266 control chromosomes in the GnomAD database, including 315 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 0.054 (315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0778 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: 0.0543 AC: 8262 AN: 152148 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0542 AC: 8256 AN: 152266 Hom.: 315 Cov.: 32 AF XY: 0.0548 AC XY: 4077 AN XY: 74444

African (AFR) AF: 0.0137 AC: 570 AN: 41562

American (AMR) AF: 0.0316 AC: 483 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1408 AN: 10580

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5411 AN: 68020

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0708 Hom.: 230

Bravo AF: 0.0451

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.28
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs7991424; hg19: chr13-46233325;