1-175150943-A-C

Variant names:

• chr1-175150943-A-C
• rs6701037
• ENST00000785604.1:n.141A>C

Variant summary

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

The ENST00000785604.1(ENSG00000302295):​n.141A>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 0.386 in 151,900 control chromosomes in the GnomAD database, including 11,923 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 0.39 (11923 hom., cov: 31)
• Consequence: ENSG00000302295 ENST00000785604.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 34 publications found

Genes affected

ENSG00000302295 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785604.1. 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
	ENSG00000302295	ENST00000785604.1		n.141A>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58572 AN: 151780 Hom.: 11920 Cov.: 31

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.386 AC: 58599 AN: 151900 Hom.: 11923 Cov.: 31 AF XY: 0.384 AC XY: 28482 AN XY: 74246

African (AFR) AF: 0.329 AC: 13606 AN: 41408

American (AMR) AF: 0.320 AC: 4884 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3464

East Asian (EAS) AF: 0.0939 AC: 484 AN: 5156

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4806

European-Finnish (FIN) AF: 0.501 AC: 5284 AN: 10556

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30926 AN: 67928

Other (OTH) AF: 0.374 AC: 787 AN: 2104

Alfa AF: 0.410 Hom.: 46052

Bravo AF: 0.367

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.76
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6701037; hg19: chr1-175120079;