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 ENST00000415580.2(ENSG00000230932):​n.195T>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 0.138 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: ENSG00000230932 ENST00000415580.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC126987		n.106081185A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230932	ENST00000415580.2	n.195T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000237480	ENST00000429608.2	n.258A>G		non_coding_transcript_exon_variant	Exon 2 of 3	3
ENSG00000237480	ENST00000655639.2	n.261A>G		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2060700; hg19: chr1-106623807;