1-236605645-G-T

Variant names:

• chr1-236605645-G-T
• rs10495381

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 0.0625 in 152,274 control chromosomes in the GnomAD database, including 766 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 0.063 (766 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 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: 0.0624 AC: 9494 AN: 152158 Hom.: 763 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0625 AC: 9523 AN: 152274 Hom.: 766 Cov.: 33 AF XY: 0.0613 AC XY: 4569 AN XY: 74482

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.0287

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.00330

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0201 Hom.: 36

Bravo AF: 0.0715

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495381; hg19: chr1-236768945;