chr10-111083650-A-C

Variant names:

• chr10-111083650-A-C
• rs34665740

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 0.0202 in 152,196 control chromosomes in the GnomAD database, including 81 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 0.020 (81 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 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: 0.0202 AC: 3075 AN: 152078 Hom.: 82 Cov.: 32

Gnomad AFR AF: 0.00512

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0141

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0202 AC: 3069 AN: 152196 Hom.: 81 Cov.: 32 AF XY: 0.0197 AC XY: 1466 AN XY: 74420

Gnomad4 AFR AF: 0.00511

Gnomad4 AMR AF: 0.0141

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.0238

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0189 Hom.: 8

Bravo AF: 0.0202

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.049
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34665740; hg19: chr10-112843408;