rs987515

Variant names:

• chr4-98752391-C-T
• rs987515

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 0.162 in 152,062 control chromosomes in the GnomAD database, including 2,746 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 0.16 (2746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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: 0.163 AC: 24691 AN: 151944 Hom.: 2750 Cov.: 32

Gnomad AFR AF: 0.0416

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.162 AC: 24673 AN: 152062 Hom.: 2746 Cov.: 32 AF XY: 0.161 AC XY: 11970 AN XY: 74310

African (AFR) AF: 0.0415 AC: 1723 AN: 41526

American (AMR) AF: 0.163 AC: 2489 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 316 AN: 3464

East Asian (EAS) AF: 0.501 AC: 2590 AN: 5168

South Asian (SAS) AF: 0.147 AC: 706 AN: 4816

European-Finnish (FIN) AF: 0.177 AC: 1865 AN: 10542

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14356 AN: 67970

Other (OTH) AF: 0.167 AC: 352 AN: 2108

Alfa AF: 0.175 Hom.: 317

Bravo AF: 0.160

Asia WGS AF: 0.290 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs987515; hg19: chr4-99673542;