rs10485212

chr6-72617630-G-A

Variant summary

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

The ENST00000649228.1(KCNQ5-DT):n.2250+221C>T 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 0.0905 in 152,230 control chromosomes in the GnomAD database, including 1,621 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 0.090 (1621 hom., cov: 33)
• Consequence: KCNQ5-DT ENST00000649228.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839

Genes affected

KCNQ5-DT (HGNC:55469): (KCNQ5 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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
KCNQ5-DT	ENST00000649228.1	n.2250+221C>T		intron_variant, non_coding_transcript_variant
KCNQ5-DT	ENST00000664828.1	n.2520+221C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13738 AN: 152112 Hom.: 1618 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.0213

Gnomad SAS AF: 0.0318

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0905 AC: 13770 AN: 152230 Hom.: 1621 Cov.: 33 AF XY: 0.0884 AC XY: 6578 AN XY: 74442

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.0212

Gnomad4 SAS AF: 0.0314

Gnomad4 FIN AF: 0.0151

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0613 Hom.: 233

Bravo AF: 0.101

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.5
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485212; hg19: chr6-73327358;