rs2037348

chr15-78361221-G-Achr15-78361221-G-Cchr15-78361221-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 0.779 in 152,064 control chromosomes in the GnomAD database, including 46,453 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 0.78 (46453 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.919 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: 0.779 AC: 118368 AN: 151946 Hom.: 46416 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.779 AC: 118462 AN: 152064 Hom.: 46453 Cov.: 31 AF XY: 0.784 AC XY: 58238 AN XY: 74320

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.816

Alfa AF: 0.796 Hom.: 68414

Bravo AF: 0.775

Asia WGS AF: 0.896 AC: 3111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.19
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037348; hg19: chr15-78653563;