rs738842

chr22-16579276-T-C

Variant summary

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

The ENST00000493696.2(KCNMB3P1):n.679-1203A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,162 control chromosomes in the GnomAD database, including 3,697 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 0.21 (3697 hom., cov: 33)
• Consequence: KCNMB3P1 ENST00000493696.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNMB3P1	ENST00000493696.2	n.679-1203A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31350 AN: 152044 Hom.: 3694 Cov.: 33

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.209

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.206 AC: 31357 AN: 152162 Hom.: 3697 Cov.: 33 AF XY: 0.208 AC XY: 15478 AN XY: 74380

Gnomad4 AFR AF: 0.0751

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.207

Alfa AF: 0.237 Hom.: 563

Bravo AF: 0.200

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.2
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738842; hg19: chr22-17060166;