rs16886849

Variant names:

• chr7-80728647-T-C
• rs16886849

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 0.134 in 152,070 control chromosomes in the GnomAD database, including 1,374 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 0.13 (1374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.202 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: 0.134 AC: 20342 AN: 151952 Hom.: 1369 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.134 AC: 20372 AN: 152070 Hom.: 1374 Cov.: 32 AF XY: 0.134 AC XY: 9949 AN XY: 74318

African (AFR) AF: 0.153 AC: 6356 AN: 41480

American (AMR) AF: 0.133 AC: 2023 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1092 AN: 5148

South Asian (SAS) AF: 0.172 AC: 827 AN: 4810

European-Finnish (FIN) AF: 0.119 AC: 1266 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8032 AN: 67988

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.123 Hom.: 2016

Bravo AF: 0.136

Asia WGS AF: 0.187 AC: 651 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	2.3
DANN	Benign	0.66
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs16886849; hg19: chr7-80357963;