chr16-50805737-T-C

Variant names:

• chr16-50805737-T-C
• rs1861762

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 0.552 in 152,022 control chromosomes in the GnomAD database, including 24,015 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 0.55 (24015 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.552 AC: 83892 AN: 151904 Hom.: 23977 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.552 AC: 83986 AN: 152022 Hom.: 24015 Cov.: 31 AF XY: 0.548 AC XY: 40734 AN XY: 74294

African (AFR) AF: 0.683 AC: 28313 AN: 41452

American (AMR) AF: 0.517 AC: 7905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2321 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1176 AN: 5166

South Asian (SAS) AF: 0.477 AC: 2303 AN: 4830

European-Finnish (FIN) AF: 0.485 AC: 5115 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35008 AN: 67952

Other (OTH) AF: 0.541 AC: 1144 AN: 2114

Alfa AF: 0.544 Hom.: 5000

Bravo AF: 0.558

Asia WGS AF: 0.384 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.27
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs1861762; hg19: chr16-50839648;