rs9636231

Variant names:

• chr2-138914385-G-A
• rs9636231
• ENST00000821989.1:n.73-3898C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-138914385-G-A
• chr2-138914385-G-T

Variant summary

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

The ENST00000821989.1(ENSG00000306916):​n.73-3898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,178 control chromosomes in the GnomAD database, including 5,246 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 0.24 (5246 hom., cov: 33)
• Consequence: ENSG00000306916 ENST00000821989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 7 publications found

Genes affected

ENSG00000306916 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821989.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306916	ENST00000821989.1		n.73-3898C>T		intron	N/A
	ENSG00000306916	ENST00000821990.1		n.292+2259C>T		intron	N/A
	ENSG00000306916	ENST00000821991.1		n.763+2259C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37236 AN: 152058 Hom.: 5240 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.245 AC: 37249 AN: 152178 Hom.: 5246 Cov.: 33 AF XY: 0.246 AC XY: 18268 AN XY: 74404

African (AFR) AF: 0.120 AC: 4990 AN: 41516

American (AMR) AF: 0.304 AC: 4643 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1429 AN: 5184

South Asian (SAS) AF: 0.172 AC: 832 AN: 4828

European-Finnish (FIN) AF: 0.346 AC: 3660 AN: 10572

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

European-Non Finnish (NFE) AF: 0.293 AC: 19955 AN: 68002

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.269 Hom.: 13042

Bravo AF: 0.239

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.011
DANN	Benign	0.41
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9636231; hg19: chr2-139671955;