chr15-48703189-G-T

Variant names:

• chr15-48703189-G-T
• rs1072994

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 0.672 in 152,048 control chromosomes in the GnomAD database, including 36,032 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 0.67 (36032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.824 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: 0.672 AC: 102136 AN: 151928 Hom.: 36034 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.672 AC: 102162 AN: 152048 Hom.: 36032 Cov.: 31 AF XY: 0.681 AC XY: 50604 AN XY: 74344

African (AFR) AF: 0.435 AC: 18046 AN: 41446

American (AMR) AF: 0.706 AC: 10782 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2499 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3883 AN: 5160

South Asian (SAS) AF: 0.846 AC: 4077 AN: 4820

European-Finnish (FIN) AF: 0.855 AC: 9051 AN: 10592

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51472 AN: 67966

Other (OTH) AF: 0.694 AC: 1465 AN: 2110

Alfa AF: 0.726 Hom.: 157145

Bravo AF: 0.649

Asia WGS AF: 0.747 AC: 2593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs1072994; hg19: chr15-48995386;