rs1074044

Variant names:

• chr13-88391071-G-A
• rs1074044

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;