rs1037398

Positions:

• chr11-80436154-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;