rs7498329

Variant names:

• chr16-28999450-A-C
• rs7498329

Your query was ambiguous. Multiple possible variants found:

• chr16-28999450-A-C
• chr16-28999450-A-T

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 0.181 in 152,008 control chromosomes in the GnomAD database, including 2,840 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 0.18 (2840 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.181 AC: 27529 AN: 151890 Hom.: 2844 Cov.: 31

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.181 AC: 27513 AN: 152008 Hom.: 2840 Cov.: 31 AF XY: 0.180 AC XY: 13386 AN XY: 74298

African (AFR) AF: 0.0900 AC: 3733 AN: 41486

American (AMR) AF: 0.215 AC: 3276 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5164

South Asian (SAS) AF: 0.0601 AC: 290 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2501 AN: 10548

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15358 AN: 67972

Other (OTH) AF: 0.194 AC: 409 AN: 2104

Alfa AF: 0.208 Hom.: 6547

Bravo AF: 0.181

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.6
DANN	Benign	0.82
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs7498329; hg19: chr16-29010771;