rs1372525

Variant names:

• chr4-89855014-G-A
• rs1372525
• ENST00000776862.1:n.113C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-89855014-G-A
• chr4-89855014-G-C
• chr4-89855014-G-T

Variant summary

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

The ENST00000776862.1(ENSG00000301182):​n.113C>T 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 0.544 in 152,022 control chromosomes in the GnomAD database, including 23,071 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 0.54 (23071 hom., cov: 32)
• Consequence: ENSG00000301182 ENST00000776862.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 8 publications found

Genes affected

ENSG00000301182 (HGNC:58852):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776862.1. 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
	ENSG00000301182	ENST00000776862.1		n.113C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000301182	ENST00000776864.1		n.139C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000301182	ENST00000776860.1		n.209-14052C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82707 AN: 151904 Hom.: 23065 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.544 AC: 82736 AN: 152022 Hom.: 23071 Cov.: 32 AF XY: 0.544 AC XY: 40380 AN XY: 74288

African (AFR) AF: 0.611 AC: 25324 AN: 41440

American (AMR) AF: 0.481 AC: 7352 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3466

East Asian (EAS) AF: 0.852 AC: 4407 AN: 5172

South Asian (SAS) AF: 0.492 AC: 2368 AN: 4812

European-Finnish (FIN) AF: 0.570 AC: 6022 AN: 10556

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34079 AN: 67972

Other (OTH) AF: 0.508 AC: 1075 AN: 2116

Alfa AF: 0.515 Hom.: 4300

Bravo AF: 0.544

Asia WGS AF: 0.652 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1372525; hg19: chr4-90776165;