chr15-48969319-A-C

Variant names:

• chr15-48969319-A-C
• rs11070672

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 0.573 in 152,106 control chromosomes in the GnomAD database, including 27,724 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 0.57 (27724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.573 AC: 87099 AN: 151988 Hom.: 27717 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.573 AC: 87135 AN: 152106 Hom.: 27724 Cov.: 32 AF XY: 0.579 AC XY: 43084 AN XY: 74350

African (AFR) AF: 0.283 AC: 11740 AN: 41482

American (AMR) AF: 0.596 AC: 9115 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3466

East Asian (EAS) AF: 0.827 AC: 4281 AN: 5174

South Asian (SAS) AF: 0.574 AC: 2766 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8064 AN: 10580

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46758 AN: 67980

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.614 Hom.: 9536

Bravo AF: 0.551

Asia WGS AF: 0.666 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11070672; hg19: chr15-49261516;