ENST00000493696.2:n.2504C>G

Variant names:

• chr22-16576248-G-C
• rs5746647
• ENST00000493696.2:n.2504C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000493696.2(KCNMB3P1):​n.2504C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNMB3P1 ENST00000493696.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 7 publications found

Genes affected

KCNMB3P1 (HGNC:6288): (KCNMB3 pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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
KCNMB3P1	ENST00000493696.2	n.2504C>G		non_coding_transcript_exon_variant	Exon 3 of 3	6

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 58156 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 26920

African (AFR) AF: 0.00 AC: 0 AN: 2672

American (AMR) AF: 0.00 AC: 0 AN: 1678

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3678

East Asian (EAS) AF: 0.00 AC: 0 AN: 8868

South Asian (SAS) AF: 0.00 AC: 0 AN: 514

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 374

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 35512

Other (OTH) AF: 0.00 AC: 0 AN: 4820

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5746647; hg19: chr22-17057138;