15-85880677-T-C

Variant names:

• chr15-85880677-T-C
• rs11634319

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 0.827 in 152,160 control chromosomes in the GnomAD database, including 52,813 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 0.83 (52813 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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 (AFR) allele frequency at 95% confidence interval = 0.948 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: 0.827 AC: 125693 AN: 152040 Hom.: 52761 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.827 AC: 125801 AN: 152160 Hom.: 52813 Cov.: 31 AF XY: 0.821 AC XY: 61081 AN XY: 74374

African (AFR) AF: 0.955 AC: 39687 AN: 41536

American (AMR) AF: 0.700 AC: 10700 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3000 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2961 AN: 5152

South Asian (SAS) AF: 0.854 AC: 4111 AN: 4812

European-Finnish (FIN) AF: 0.731 AC: 7735 AN: 10586

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54701 AN: 68002

Other (OTH) AF: 0.840 AC: 1772 AN: 2110

Alfa AF: 0.800 Hom.: 26508

Bravo AF: 0.822

Asia WGS AF: 0.754 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11634319; hg19: chr15-86423908;