rs884483

Variant names:

• chr15-70109970-T-C
• rs884483

Your query was ambiguous. Multiple possible variants found:

• chr15-70109970-T-C
• chr15-70109970-T-G

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 0.117 in 151,808 control chromosomes in the GnomAD database, including 1,089 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 0.12 (1089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 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: 0.117 AC: 17817 AN: 151688 Hom.: 1087 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.117 AC: 17831 AN: 151808 Hom.: 1089 Cov.: 32 AF XY: 0.119 AC XY: 8818 AN XY: 74184

African (AFR) AF: 0.124 AC: 5139 AN: 41394

American (AMR) AF: 0.0919 AC: 1402 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3466

East Asian (EAS) AF: 0.159 AC: 820 AN: 5144

South Asian (SAS) AF: 0.203 AC: 976 AN: 4806

European-Finnish (FIN) AF: 0.112 AC: 1185 AN: 10536

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7449 AN: 67900

Other (OTH) AF: 0.111 AC: 233 AN: 2106

Alfa AF: 0.113 Hom.: 3219

Bravo AF: 0.114

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.38
DANN	Benign	0.86
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs884483; hg19: chr15-70402309;