4-130044017-C-T

Variant names:

• chr4-130044017-C-T
• rs1395976
• ENST00000839037.1:n.434+10919C>T

Variant summary

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

The ENST00000839037.1(ENSG00000309145):​n.434+10919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,126 control chromosomes in the GnomAD database, including 4,540 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 0.15 (4540 hom., cov: 32)
• Consequence: ENSG00000309145 ENST00000839037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 1 publications found

Genes affected

ENSG00000309145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839037.1. 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
	ENSG00000309145	ENST00000839037.1		n.434+10919C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22558 AN: 152010 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.149 AC: 22620 AN: 152126 Hom.: 4540 Cov.: 32 AF XY: 0.146 AC XY: 10884 AN XY: 74368

African (AFR) AF: 0.459 AC: 18999 AN: 41434

American (AMR) AF: 0.0903 AC: 1381 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3470

East Asian (EAS) AF: 0.0714 AC: 369 AN: 5166

South Asian (SAS) AF: 0.0468 AC: 226 AN: 4824

European-Finnish (FIN) AF: 0.0581 AC: 616 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 736 AN: 68022

Other (OTH) AF: 0.121 AC: 255 AN: 2110

Alfa AF: 0.0260 Hom.: 117

Bravo AF: 0.164

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1395976; hg19: chr4-130965172;