rs10197319

Variant names:

• chr2-203898321-G-A
• rs10197319

Your query was ambiguous. Multiple possible variants found:

• chr2-203898321-G-A
• chr2-203898321-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 0.437 in 151,976 control chromosomes in the GnomAD database, including 14,790 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 0.44 (14790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

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 (SAS) allele frequency at 95% confidence interval = 0.501 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: 0.437 AC: 66325 AN: 151856 Hom.: 14784 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.437 AC: 66355 AN: 151976 Hom.: 14790 Cov.: 32 AF XY: 0.432 AC XY: 32123 AN XY: 74288

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.462

Alfa AF: 0.465 Hom.: 33156

Bravo AF: 0.438

Asia WGS AF: 0.410 AC: 1426 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	0.57
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10197319; hg19: chr2-204763044;