rs1319435

Variant names:

• chr1-209874273-T-C
• rs1319435

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 0.106 in 152,234 control chromosomes in the GnomAD database, including 1,134 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 0.11 (1134 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 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: 0.106 AC: 16168 AN: 152116 Hom.: 1136 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.106 AC: 16162 AN: 152234 Hom.: 1134 Cov.: 32 AF XY: 0.104 AC XY: 7725 AN XY: 74422

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.0438

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.105

Alfa AF: 0.124 Hom.: 516

Bravo AF: 0.100

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319435; hg19: chr1-210047618;