chr15-95975881-T-C

Variant names:

• chr15-95975881-T-C
• rs4984470

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 0.068 in 149,778 control chromosomes in the GnomAD database, including 920 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 0.068 (920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10152 AN: 149656 Hom.: 918 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00222

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0160

Gnomad EAS AF: 0.00384

Gnomad SAS AF: 0.0217

Gnomad FIN AF: 0.00134

Gnomad MID AF: 0.0400

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0680 AC: 10178 AN: 149778 Hom.: 920 Cov.: 32 AF XY: 0.0649 AC XY: 4751 AN XY: 73172

African (AFR) AF: 0.209 AC: 8531 AN: 40814

American (AMR) AF: 0.0300 AC: 453 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.0160 AC: 55 AN: 3432

East Asian (EAS) AF: 0.00405 AC: 20 AN: 4936

South Asian (SAS) AF: 0.0215 AC: 101 AN: 4698

European-Finnish (FIN) AF: 0.00134 AC: 14 AN: 10460

Middle Eastern (MID) AF: 0.0461 AC: 13 AN: 282

European-Non Finnish (NFE) AF: 0.0130 AC: 869 AN: 67080

Other (OTH) AF: 0.0577 AC: 120 AN: 2078

Alfa AF: 0.0342 Hom.: 474

Bravo AF: 0.0757

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4984470; hg19: chr15-96519110;