ENST00000844237.1:n.311C>T

Variant names:

• chr7-4383169-G-A
• rs73034881
• ENST00000844237.1:n.311C>T

Variant summary

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

The ENST00000844237.1(ENSG00000309840):​n.311C>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 0.117 in 152,082 control chromosomes in the GnomAD database, including 1,052 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 0.12 (1052 hom., cov: 32)
• Consequence: ENSG00000309840 ENST00000844237.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 1 publications found

Genes affected

ENSG00000309840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844237.1. 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
	ENSG00000309840	ENST00000844237.1		n.311C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17736 AN: 151964 Hom.: 1046 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.117 AC: 17766 AN: 152082 Hom.: 1052 Cov.: 32 AF XY: 0.116 AC XY: 8591 AN XY: 74344

African (AFR) AF: 0.118 AC: 4878 AN: 41462

American (AMR) AF: 0.0989 AC: 1511 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3472

East Asian (EAS) AF: 0.0884 AC: 457 AN: 5170

South Asian (SAS) AF: 0.0539 AC: 260 AN: 4820

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8617 AN: 67982

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.118 Hom.: 198

Bravo AF: 0.117

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.51
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs73034881; hg19: chr7-4422800;