22-16576248-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000493696.2(KCNMB3P1):​n.2504C>A 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 0.897 in 152,036 control chromosomes in the GnomAD database, including 61,702 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 0.90 (61702 hom., cov: 30)
  • Exomes 𝑓: 0.94 (25796 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNMB3P1 ENST00000493696.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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
KCNMB3P1	ENST00000493696.2	n.2504C>A		non_coding_transcript_exon_variant	Exon 3 of 3	6

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136246 AN: 151918 Hom.: 61664 Cov.: 30

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.917

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.941 AC: 54676 AN: 58114 Hom.: 25796 Cov.: 0 AF XY: 0.940 AC XY: 25276 AN XY: 26902

Gnomad4 AFR exome AF: 0.761

Gnomad4 AMR exome AF: 0.948

Gnomad4 ASJ exome AF: 0.925

Gnomad4 EAS exome AF: 0.988

Gnomad4 SAS exome AF: 0.936

Gnomad4 FIN exome AF: 0.950

Gnomad4 NFE exome AF: 0.946

Gnomad4 OTH exome AF: 0.923

GnomAD4 genome AF: 0.897 AC: 136342 AN: 152036 Hom.: 61702 Cov.: 30 AF XY: 0.898 AC XY: 66763 AN XY: 74338

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.918

Alfa AF: 0.943 Hom.: 125878

Bravo AF: 0.891

Asia WGS AF: 0.954 AC: 3314 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5746647; hg19: chr22-17057138;