rs1037398

Variant names:

• chr11-80436154-G-C
• rs1037398

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 0.635 in 152,002 control chromosomes in the GnomAD database, including 31,332 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 0.63 (31332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 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: 0.635 AC: 96372 AN: 151884 Hom.: 31272 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.635 AC: 96500 AN: 152002 Hom.: 31332 Cov.: 32 AF XY: 0.639 AC XY: 47440 AN XY: 74286

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.603

Alfa AF: 0.597 Hom.: 3416

Bravo AF: 0.638

Asia WGS AF: 0.589 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037398; hg19: chr11-80147198;