chr1-169104108-G-A

Variant names:

• chr1-169104108-G-A
• rs1320976
• ENST00000415637.2:n.32G>A

Variant summary

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

The ENST00000415637.2(ENSG00000237707):​n.32G>A 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 0.169 in 152,254 control chromosomes in the GnomAD database, including 2,451 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 0.17 (2450 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: ENSG00000237707 ENST00000415637.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 20 publications found

Genes affected

ENSG00000237707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415637.2. 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
	LOC101928596	NR_135799.1		n.-16G>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237707	ENST00000415637.2	TSL:2	n.32G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000237707	ENST00000781189.1		n.101+34G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25650 AN: 152028 Hom.: 2448 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.139 AC: 15 AN: 108 Hom.: 1 Cov.: 0 AF XY: 0.167 AC XY: 14 AN XY: 84

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.134 AC: 11 AN: 82

Other (OTH) AF: 0.300 AC: 3 AN: 10

GnomAD4 genome AF: 0.169 AC: 25688 AN: 152146 Hom.: 2450 Cov.: 32 AF XY: 0.170 AC XY: 12624 AN XY: 74370

African (AFR) AF: 0.261 AC: 10822 AN: 41480

American (AMR) AF: 0.161 AC: 2454 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.133 AC: 689 AN: 5180

South Asian (SAS) AF: 0.114 AC: 549 AN: 4826

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10582

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8304 AN: 68012

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.140 Hom.: 4486

Bravo AF: 0.172

Asia WGS AF: 0.141 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.0
DANN	Benign	0.84
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1320976; hg19: chr1-169073346;