rs9937239

Variant names:

• chr16-87073514-G-A
• rs9937239
• ENST00000767853.1:n.304+1131C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-87073514-G-A
• chr16-87073514-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000767853.1(ENSG00000289336):​n.304+1131C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,066 control chromosomes in the GnomAD database, including 7,046 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 0.30 (7046 hom., cov: 33)
• Consequence: ENSG00000289336 ENST00000767853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 publications found

Genes affected

ENSG00000289336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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
ENSG00000289336	ENST00000767853.1	n.304+1131C>T		intron_variant	Intron 1 of 1
ENSG00000289336	ENST00000767854.1	n.154+1131C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45192 AN: 151948 Hom.: 7033 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.297 AC: 45226 AN: 152066 Hom.: 7046 Cov.: 33 AF XY: 0.300 AC XY: 22321 AN XY: 74304

African (AFR) AF: 0.376 AC: 15592 AN: 41470

American (AMR) AF: 0.278 AC: 4252 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5182

South Asian (SAS) AF: 0.404 AC: 1951 AN: 4828

European-Finnish (FIN) AF: 0.334 AC: 3519 AN: 10546

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16776 AN: 67978

Other (OTH) AF: 0.276 AC: 581 AN: 2108

Alfa AF: 0.255 Hom.: 9430

Bravo AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9937239; hg19: chr16-87107120;