ENST00000606194.1:n.169G>C

Variant names:

• chr5-10266978-C-G
• rs2662532
• ENST00000606194.1:n.169G>C

Variant summary

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

The ENST00000606194.1(ENSG00000271980):​n.169G>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 0.739 in 151,908 control chromosomes in the GnomAD database, including 43,610 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 0.74 (43606 hom., cov: 32)
  • Exomes 𝑓: 0.79 (4 hom.)
• Consequence: ENSG00000271980 ENST00000606194.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 11 publications found

Genes affected

ENSG00000271980 (HGNC:58210):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271980	ENST00000606194.1	n.169G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112139 AN: 151778 Hom.: 43592 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.767

GnomAD4 exome AF: 0.786 AC: 11 AN: 14 Hom.: 4 Cov.: 0 AF XY: 0.786 AC XY: 11 AN XY: 14

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 6 AN: 8

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.739 AC: 112192 AN: 151894 Hom.: 43606 Cov.: 32 AF XY: 0.742 AC XY: 55090 AN XY: 74256

African (AFR) AF: 0.465 AC: 19180 AN: 41214

American (AMR) AF: 0.809 AC: 12375 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3044 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4473 AN: 5168

South Asian (SAS) AF: 0.664 AC: 3206 AN: 4826

European-Finnish (FIN) AF: 0.858 AC: 9102 AN: 10604

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58193 AN: 68008

Other (OTH) AF: 0.767 AC: 1616 AN: 2106

Alfa AF: 0.783 Hom.: 6018

Bravo AF: 0.726

Asia WGS AF: 0.770 AC: 2677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2662532; hg19: chr5-10267090;