rs2662532

Positions:

• chr5-10266978-C-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000606194.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000606194.1	n.169G>C		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.767

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2662532; hg19: chr5-10267090;