rs1317209

Positions:

• chr1-19813543-G-A
• chr1-19813543-G-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 0.236 in 152,110 control chromosomes in the GnomAD database, including 4,415 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 0.24 (4415 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.236 AC: 35880 AN: 151992 Hom.: 4407 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.236 AC: 35925 AN: 152110 Hom.: 4415 Cov.: 32 AF XY: 0.243 AC XY: 18056 AN XY: 74348

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.237

Alfa AF: 0.199 Hom.: 7261

Bravo AF: 0.240

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317209; hg19: chr1-20140036;