16-1023552-A-G

Variant names:

• chr16-1023552-A-G
• rs2744148

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 0.153 in 151,994 control chromosomes in the GnomAD database, including 1,921 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 0.15 (1921 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 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: 0.153 AC: 23210 AN: 151876 Hom.: 1924 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.153 AC: 23222 AN: 151994 Hom.: 1921 Cov.: 33 AF XY: 0.150 AC XY: 11145 AN XY: 74300

African (AFR) AF: 0.149 AC: 6159 AN: 41454

American (AMR) AF: 0.119 AC: 1817 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3468

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5164

South Asian (SAS) AF: 0.300 AC: 1448 AN: 4822

European-Finnish (FIN) AF: 0.0847 AC: 896 AN: 10582

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11520 AN: 67920

Other (OTH) AF: 0.170 AC: 358 AN: 2102

Alfa AF: 0.167 Hom.: 8679

Bravo AF: 0.151

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.55
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2744148; hg19: chr16-1073552; COSMIC: COSV60067604;