rs7991424

Positions:

• chr13-45659190-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0604 Hom.: 27

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7991424; hg19: chr13-46233325;