1-58584660-A-G

Variant names:

• chr1-58584660-A-G
• rs6690139
• ENST00000767260.1:n.191T>C

Variant summary

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

The ENST00000767260.1(ENSG00000299892):​n.191T>C 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 0.147 in 152,132 control chromosomes in the GnomAD database, including 1,699 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 (1699 hom., cov: 32)
• Consequence: ENSG00000299892 ENST00000767260.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 19 publications found

Genes affected

ENSG00000299892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767260.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299892	ENST00000767260.1		n.191T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000283445	ENST00000637377.2	TSL:5	n.161+8284A>G		intron	N/A
	ENSG00000283445	ENST00000767021.1		n.188+8284A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22274 AN: 152014 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.147 AC: 22288 AN: 152132 Hom.: 1699 Cov.: 32 AF XY: 0.141 AC XY: 10463 AN XY: 74370

African (AFR) AF: 0.134 AC: 5582 AN: 41506

American (AMR) AF: 0.122 AC: 1863 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3468

East Asian (EAS) AF: 0.0522 AC: 270 AN: 5174

South Asian (SAS) AF: 0.139 AC: 669 AN: 4814

European-Finnish (FIN) AF: 0.0934 AC: 989 AN: 10586

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11704 AN: 67984

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.148 Hom.: 963

Bravo AF: 0.148

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6690139; hg19: chr1-59050332; COSMIC: COSV59945409;