rs1374313

chr2-119388079-T-C

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 0.551 in 152,094 control chromosomes in the GnomAD database, including 24,281 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 0.55 (24281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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 = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83773 AN: 151976 Hom.: 24234 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.551 AC: 83873 AN: 152094 Hom.: 24281 Cov.: 33 AF XY: 0.547 AC XY: 40630 AN XY: 74334

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.523

Alfa AF: 0.499 Hom.: 31799

Bravo AF: 0.554

Asia WGS AF: 0.410 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.25
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374313; hg19: chr2-120145655;