rs2122339

Variant names:

• chr4-27692567-T-A
• rs2122339
• ENST00000814935.1:n.202T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-27692567-T-A
• chr4-27692567-T-C

Variant summary

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

The ENST00000814935.1(ENSG00000306044):​n.202T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 152,086 control chromosomes in the GnomAD database, including 139 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 0.024 (139 hom., cov: 33)
• Consequence: ENSG00000306044 ENST00000814935.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

Genes affected

ENSG00000306044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374548	XR_925517.2	n.146-2220T>A		intron_variant	Intron 1 of 4
LOC105374548	XR_925518.2	n.146-2220T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306044	ENST00000814935.1	n.202T>A		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000306044	ENST00000814936.1	n.202T>A		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3658 AN: 151968 Hom.: 136 Cov.: 33

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0256

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00922

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0241 AC: 3668 AN: 152086 Hom.: 139 Cov.: 33 AF XY: 0.0270 AC XY: 2006 AN XY: 74332

African (AFR) AF: 0.0160 AC: 662 AN: 41498

American (AMR) AF: 0.0761 AC: 1163 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3470

East Asian (EAS) AF: 0.139 AC: 712 AN: 5128

South Asian (SAS) AF: 0.0254 AC: 122 AN: 4808

European-Finnish (FIN) AF: 0.0286 AC: 303 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00922 AC: 627 AN: 67982

Other (OTH) AF: 0.0284 AC: 60 AN: 2114

Alfa AF: 0.00512 Hom.: 1

Bravo AF: 0.0287

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.6
DANN	Benign	0.91
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2122339; hg19: chr4-27694189;