ENST00000806560.1:n.1120C>T

Variant names:

• chr6-37756637-C-T
• rs747158
• ENST00000806560.1:n.1120C>T

Variant summary

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

The ENST00000806560.1(ENSG00000304838):​n.1120C>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 0.0995 in 152,266 control chromosomes in the GnomAD database, including 1,071 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 0.10 (1071 hom., cov: 32)
• Consequence: ENSG00000304838 ENST00000806560.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 3 publications found

Genes affected

ENSG00000304838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806560.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304838	ENST00000806560.1		n.1120C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15151 AN: 152148 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.0995 AC: 15151 AN: 152266 Hom.: 1071 Cov.: 32 AF XY: 0.0950 AC XY: 7071 AN XY: 74446

African (AFR) AF: 0.0258 AC: 1073 AN: 41564

American (AMR) AF: 0.0953 AC: 1459 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5188

South Asian (SAS) AF: 0.0353 AC: 170 AN: 4818

European-Finnish (FIN) AF: 0.100 AC: 1065 AN: 10610

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10046 AN: 67994

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.131 Hom.: 843

Bravo AF: 0.0999

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs747158; hg19: chr6-37724413;