rs1074044

Positions:

• chr13-88391071-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 0.591 in 151,672 control chromosomes in the GnomAD database, including 27,006 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 0.59 (27006 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89495 AN: 151554 Hom.: 26989 Cov.: 30

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.591 AC: 89563 AN: 151672 Hom.: 27006 Cov.: 30 AF XY: 0.594 AC XY: 44025 AN XY: 74078

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.608

Alfa AF: 0.545 Hom.: 10447

Bravo AF: 0.606

Asia WGS AF: 0.594 AC: 2063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074044; hg19: chr13-89043326;