rs1372108

Variant names:

• chr11-71254030-G-A
• rs1372108

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 0.0837 in 151,670 control chromosomes in the GnomAD database, including 1,514 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 0.084 (1514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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: 0.0834 AC: 12640 AN: 151552 Hom.: 1502 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.00180

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00927

Gnomad OTH AF: 0.0644

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

GnomAD4 genome AF: 0.0837 AC: 12700 AN: 151670 Hom.: 1514 Cov.: 31 AF XY: 0.0809 AC XY: 5997 AN XY: 74120

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.0672

Gnomad4 FIN AF: 0.00180

Gnomad4 NFE AF: 0.00927

Gnomad4 OTH AF: 0.0685

Alfa AF: 0.0656 Hom.: 104

Bravo AF: 0.0931

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372108; hg19: chr11-70965076;