1-235903172-T-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786960.1. 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
	ENSG00000302457	ENST00000786960.1		n.395T>G		non_coding_transcript_exon	Exon 4 of 5
	ENSG00000302457	ENST00000786961.1		n.395T>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000302457	ENST00000786952.1		n.209+9942T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6665519;

hg19: chr1-236066472;