rs1341015

Positions:

• chr1-119438426-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 0.141 in 152,202 control chromosomes in the GnomAD database, including 2,187 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 0.14 (2187 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

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 (AFR) allele frequency at 95% confidence interval = 0.277 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: 0.141 AC: 21490 AN: 152084 Hom.: 2183 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.141 AC: 21519 AN: 152202 Hom.: 2187 Cov.: 33 AF XY: 0.140 AC XY: 10415 AN XY: 74424

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0679

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.146

Alfa AF: 0.105 Hom.: 841

Bravo AF: 0.156

Asia WGS AF: 0.107 AC: 375 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341015; hg19: chr1-119981049;