rs16903544

Variant names:

• chr8-128632988-T-C
• rs16903544

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 0.0993 in 151,978 control chromosomes in the GnomAD database, including 744 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 0.099 (744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 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: 0.0992 AC: 15066 AN: 151860 Hom.: 739 Cov.: 32

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0993 AC: 15088 AN: 151978 Hom.: 744 Cov.: 32 AF XY: 0.0996 AC XY: 7400 AN XY: 74272

African (AFR) AF: 0.0927 AC: 3843 AN: 41446

American (AMR) AF: 0.0833 AC: 1271 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3472

East Asian (EAS) AF: 0.134 AC: 690 AN: 5158

South Asian (SAS) AF: 0.110 AC: 527 AN: 4810

European-Finnish (FIN) AF: 0.0888 AC: 938 AN: 10562

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7201 AN: 67956

Other (OTH) AF: 0.107 AC: 224 AN: 2102

Alfa AF: 0.101 Hom.: 98

Bravo AF: 0.0985

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs16903544; hg19: chr8-129645234;