4-9144727-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369250	XR_001741580.3	n.1087A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105369250	XR_001741581.3	n.1180A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105369250	XR_001741583.3	n.1083A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288075	ENST00000810937.1	n.1189A>G		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000288075	ENST00000810947.1	n.765A>G		non_coding_transcript_exon_variant	Exon 5 of 6
ENSG00000288075	ENST00000810948.1	n.688A>G		non_coding_transcript_exon_variant	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 v4.3

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;