chr4-9144727-T-C

Variant names:

• chr4-9144727-T-C
• rs1988623
• ENST00000810937.1:n.1189A>G

Variant summary

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

The ENST00000810937.1(ENSG00000288075):​n.1189A>G 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 0.413 in 151,844 control chromosomes in the GnomAD database, including 15,556 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 0.41 (15556 hom., cov: 33)
• Consequence: ENSG00000288075 ENST00000810937.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 publications found

Genes affected

ENSG00000288075 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810937.1. 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
	ENSG00000288075	ENST00000810937.1		n.1189A>G		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000288075	ENST00000810947.1		n.765A>G		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000288075	ENST00000810948.1		n.688A>G		non_coding_transcript_exon	Exon 4 of 6

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62622 AN: 151728 Hom.: 15500 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.413 AC: 62746 AN: 151844 Hom.: 15556 Cov.: 33 AF XY: 0.413 AC XY: 30637 AN XY: 74206

African (AFR) AF: 0.705 AC: 29217 AN: 41414

American (AMR) AF: 0.405 AC: 6175 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3466

East Asian (EAS) AF: 0.306 AC: 1574 AN: 5142

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4818

European-Finnish (FIN) AF: 0.306 AC: 3224 AN: 10532

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18578 AN: 67900

Other (OTH) AF: 0.389 AC: 822 AN: 2114

Alfa AF: 0.176 Hom.: 308

Bravo AF: 0.430

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.20
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1988623; hg19: chr4-9146453;