rs1416131

Variant names:

• chr10-113433539-A-G
• rs1416131

Your query was ambiguous. Multiple possible variants found:

• chr10-113433539-A-G
• chr10-113433539-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;