rs6574994

Variant names:

• chr14-88148197-A-G
• rs6574994
• ENST00000556546.2:n.334-10132T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556546.2(ENSG00000258975):​n.334-10132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,094 control chromosomes in the GnomAD database, including 34,533 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 0.66 (34533 hom., cov: 32)
• Consequence: ENSG00000258975 ENST00000556546.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

Genes affected

ENSG00000258975 (HGNC:):

KCNK10-AS1 (HGNC:58074):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556546.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258975	ENST00000556546.2	TSL:3	n.334-10132T>C		intron	N/A
	ENSG00000258975	ENST00000703508.1		n.73-10132T>C		intron	N/A
	ENSG00000258975	ENST00000703510.1		n.421-10132T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100150 AN: 151976 Hom.: 34474 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.659 AC: 100271 AN: 152094 Hom.: 34533 Cov.: 32 AF XY: 0.653 AC XY: 48583 AN XY: 74356

African (AFR) AF: 0.874 AC: 36309 AN: 41526

American (AMR) AF: 0.596 AC: 9109 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2340 AN: 5148

South Asian (SAS) AF: 0.542 AC: 2612 AN: 4822

European-Finnish (FIN) AF: 0.577 AC: 6096 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39806 AN: 67964

Other (OTH) AF: 0.625 AC: 1318 AN: 2110

Alfa AF: 0.600 Hom.: 44403

Bravo AF: 0.668

Asia WGS AF: 0.583 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6574994; hg19: chr14-88614541;