rs2060700

Variant names:

• chr1-106081185-A-G
• rs2060700
• ENST00000415580.2:n.195T>C

Variant summary

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

The ENST00000429608.2(ENSG00000237480):​n.258A>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 0.138 in 1,558,114 control chromosomes in the GnomAD database, including 18,335 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 (2636 hom., cov: 32)
  • Exomes 𝑓: 0.13 (15699 hom.)
• Consequence: ENSG00000237480 ENST00000429608.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.885
• Publications: 8 publications found

Genes affected

ENSG00000230932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429608.2. 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
	ENSG00000230932	ENST00000415580.2	TSL:6	n.195T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000237480	ENST00000429608.2	TSL:3	n.258A>G		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000237480	ENST00000655639.2		n.261A>G		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26221 AN: 152060 Hom.: 2622 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.134 AC: 188871 AN: 1405936 Hom.: 15699 Cov.: 29 AF XY: 0.135 AC XY: 93945 AN XY: 696554

African (AFR) AF: 0.239 AC: 7715 AN: 32228

American (AMR) AF: 0.291 AC: 11154 AN: 38366

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 2664 AN: 25284

East Asian (EAS) AF: 0.421 AC: 15802 AN: 37508

South Asian (SAS) AF: 0.172 AC: 13952 AN: 80914

European-Finnish (FIN) AF: 0.123 AC: 6122 AN: 49806

Middle Eastern (MID) AF: 0.160 AC: 687 AN: 4306

European-Non Finnish (NFE) AF: 0.113 AC: 122086 AN: 1079138

Other (OTH) AF: 0.149 AC: 8689 AN: 58386

GnomAD4 genome AF: 0.173 AC: 26282 AN: 152178 Hom.: 2636 Cov.: 32 AF XY: 0.175 AC XY: 13034 AN XY: 74392

African (AFR) AF: 0.234 AC: 9699 AN: 41510

American (AMR) AF: 0.215 AC: 3280 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.418 AC: 2151 AN: 5144

South Asian (SAS) AF: 0.181 AC: 874 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10608

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8146 AN: 68014

Other (OTH) AF: 0.153 AC: 323 AN: 2110

Alfa AF: 0.158 Hom.: 299

Bravo AF: 0.186

Asia WGS AF: 0.259 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.8
DANN	Benign	0.57
PhyloP100		0.89

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: rs2060700;

hg19: chr1-106623807;