rs1416131

chr10-113433539-A-Gchr10-113433539-A-T

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 0.33 in 151,934 control chromosomes in the GnomAD database, including 8,417 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 0.33 (8417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50087 AN: 151816 Hom.: 8407 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.330 AC: 50132 AN: 151934 Hom.: 8417 Cov.: 32 AF XY: 0.324 AC XY: 24063 AN XY: 74262

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.328

Alfa AF: 0.309 Hom.: 1176

Bravo AF: 0.331

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.1
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1416131; hg19: chr10-115193298;