ENST00000786960.1:n.395T>G

Variant names:

• chr1-235903172-T-G
• rs6665519
• ENST00000786960.1:n.395T>G

Variant summary

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

The ENST00000786960.1(ENSG00000302457):​n.395T>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 0.912 in 150,090 control chromosomes in the GnomAD database, including 62,619 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 0.91 (62619 hom., cov: 24)
• Consequence: ENSG00000302457 ENST00000786960.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 4 publications found

Genes affected

ENSG00000302457 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373215	XR_001738543.2	n.534T>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105373215	XR_001738537.2	n.519+9942T>G		intron_variant	Intron 2 of 2
LOC105373215	XR_001738539.2	n.519+9942T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302457	ENST00000786960.1	n.395T>G		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000302457	ENST00000786961.1	n.395T>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000302457	ENST00000786952.1	n.209+9942T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.912 AC: 136800 AN: 149974 Hom.: 62558 Cov.: 24

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.912 AC: 136920 AN: 150090 Hom.: 62619 Cov.: 24 AF XY: 0.915 AC XY: 66818 AN XY: 73054

African (AFR) AF: 0.966 AC: 39321 AN: 40708

American (AMR) AF: 0.920 AC: 13831 AN: 15034

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2794 AN: 3462

East Asian (EAS) AF: 0.999 AC: 5094 AN: 5100

South Asian (SAS) AF: 0.967 AC: 4514 AN: 4666

European-Finnish (FIN) AF: 0.905 AC: 9157 AN: 10116

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59262 AN: 67714

Other (OTH) AF: 0.897 AC: 1875 AN: 2090

Alfa AF: 0.894 Hom.: 6161

Bravo AF: 0.915

Asia WGS AF: 0.976 AC: 3390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.53
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6665519; hg19: chr1-236066472;