chr10-111760180-A-G

Position:

• chr10-111760180-A-G

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 0.879 in 152,146 control chromosomes in the GnomAD database, including 59,206 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 0.88 (59206 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.942 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: 0.879 AC: 133666 AN: 152028 Hom.: 59175 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.879 AC: 133745 AN: 152146 Hom.: 59206 Cov.: 33 AF XY: 0.876 AC XY: 65153 AN XY: 74362

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.948

Gnomad4 OTH AF: 0.872

Alfa AF: 0.910 Hom.: 7851

Bravo AF: 0.871

Asia WGS AF: 0.769 AC: 2675 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085622; hg19: chr10-113519938;