chr16-16636871-T-G

Variant names:

• chr16-16636871-T-G
• rs9937036
• ENST00000567465.2:n.88-11473T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000567465.2(ENSG00000260126):​n.88-11473T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.017 (0 hom., cov: 0)
• Consequence: ENSG00000260126 ENST00000567465.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 3 publications found

Genes affected

ENSG00000260126 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567465.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260126	ENST00000567465.2	TSL:3	n.88-11473T>G		intron	N/A
	ENSG00000260126	ENST00000840420.1		n.82-11473T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0172 AC: 139 AN: 8096 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00818

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00150

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00228

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0172 AC: 139 AN: 8096 Hom.: 0 Cov.: 0 AF XY: 0.0154 AC XY: 61 AN XY: 3958

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0922 AC: 118 AN: 1280

American (AMR) AF: 0.00818 AC: 8 AN: 978

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 206

East Asian (EAS) AF: 0.00 AC: 0 AN: 192

South Asian (SAS) AF: 0.00 AC: 0 AN: 212

European-Finnish (FIN) AF: 0.00150 AC: 1 AN: 666

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 18

European-Non Finnish (NFE) AF: 0.00228 AC: 10 AN: 4388

Other (OTH) AF: 0.0196 AC: 2 AN: 102

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0245 Hom.: 4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs9937036; hg19: chr16-16730728;