rs1640923

Variant names:

• chr16-11227120-A-G
• rs1640923

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 0.198 in 152,058 control chromosomes in the GnomAD database, including 3,623 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 0.20 (3623 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.198 AC: 30068 AN: 151940 Hom.: 3601 Cov.: 30

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.198 AC: 30124 AN: 152058 Hom.: 3623 Cov.: 30 AF XY: 0.203 AC XY: 15077 AN XY: 74320

African (AFR) AF: 0.232 AC: 9621 AN: 41492

American (AMR) AF: 0.306 AC: 4674 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2089 AN: 5118

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4814

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10588

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9712 AN: 67988

Other (OTH) AF: 0.162 AC: 342 AN: 2110

Alfa AF: 0.180 Hom.: 364

Bravo AF: 0.214

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1640923; hg19: chr16-11320977;