15-77872364-T-C

Variant names:

• chr15-77872364-T-C
• rs11857176

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 0.49 in 151,908 control chromosomes in the GnomAD database, including 19,439 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 0.49 (19439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.489 AC: 74267 AN: 151790 Hom.: 19401 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.490 AC: 74363 AN: 151908 Hom.: 19439 Cov.: 32 AF XY: 0.486 AC XY: 36105 AN XY: 74240

African (AFR) AF: 0.693 AC: 28707 AN: 41420

American (AMR) AF: 0.459 AC: 7013 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2333 AN: 5146

South Asian (SAS) AF: 0.320 AC: 1539 AN: 4812

European-Finnish (FIN) AF: 0.407 AC: 4292 AN: 10540

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27600 AN: 67920

Other (OTH) AF: 0.441 AC: 928 AN: 2106

Alfa AF: 0.426 Hom.: 19805

Bravo AF: 0.505

Asia WGS AF: 0.389 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.53
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11857176; hg19: chr15-78164706;