rs8060871

Variant names:

• chr16-54503696-T-C
• rs8060871

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 0.137 in 152,186 control chromosomes in the GnomAD database, including 1,749 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 0.14 (1749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.137 AC: 20760 AN: 152068 Hom.: 1748 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.137 AC: 20775 AN: 152186 Hom.: 1749 Cov.: 32 AF XY: 0.136 AC XY: 10111 AN XY: 74406

African (AFR) AF: 0.228 AC: 9476 AN: 41486

American (AMR) AF: 0.104 AC: 1592 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0308 AC: 107 AN: 3472

East Asian (EAS) AF: 0.0257 AC: 133 AN: 5166

South Asian (SAS) AF: 0.107 AC: 515 AN: 4826

European-Finnish (FIN) AF: 0.137 AC: 1458 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7153 AN: 68022

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.113 Hom.: 4293

Bravo AF: 0.137

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.24
DANN	Benign	0.39
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs8060871; hg19: chr16-54537608;