22-16576248-G-T

Position:

• chr22-16576248-G-T

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:):

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/exons	MANE	Protein	UniProt
		n.16576248G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNMB3P1	ENST00000493696.2	n.2504C>A		non_coding_transcript_exon_variant	3/3	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;