rs1317209

Variant names:

• chr1-19813543-G-A
• rs1317209

Your query was ambiguous. Multiple possible variants found:

• chr1-19813543-G-A
• chr1-19813543-G-C
• chr1-19813543-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.288 AC: 11959 AN: 41506

American (AMR) AF: 0.281 AC: 4288 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3464

East Asian (EAS) AF: 0.380 AC: 1963 AN: 5166

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2478 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12369 AN: 68002

Other (OTH) AF: 0.237 AC: 497 AN: 2100

Alfa AF: 0.202 Hom.: 15340

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
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1317209; hg19: chr1-20140036;