chr1-159999218-C-T

Variant names:

• chr1-159999218-C-T
• rs6676862
• XR_007066682.1:n.1548G>A

Variant summary

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

The XR_007066682.1(LOC124904436):​n.1548G>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 0.204 in 384,180 control chromosomes in the GnomAD database, including 8,637 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 0.22 (4009 hom., cov: 31)
  • Exomes 𝑓: 0.19 (4628 hom.)
• Consequence: LOC124904436 XR_007066682.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 6 publications found

Genes affected

LOC124904436 (HGNC:):

KCNJ10 (HGNC:6256): (potassium inwardly rectifying channel subfamily J member 10) This gene encodes a member of the inward rectifier-type potassium channel family, characterized by having a greater tendency to allow potassium to flow into, rather than out of, a cell. The encoded protein may form a heterodimer with another potassium channel protein and may be responsible for the potassium buffering action of glial cells in the brain. Mutations in this gene have been associated with seizure susceptibility of common idiopathic generalized epilepsy syndromes. [provided by RefSeq, Jul 2008]

LINC01133 (HGNC:49447): (long intergenic non-protein coding RNA 1133)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904436	XR_007066682.1	n.1548G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNJ10	ENST00000639408.2	c.*240G>A		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000491635.1
KCNJ10	ENST00000637644.1	c.*251G>A		3_prime_UTR_variant	Exon 3 of 3	5		ENSP00000490282.1
KCNJ10	ENST00000640914.1	c.*308G>A		3_prime_UTR_variant	Exon 3 of 3	5		ENSP00000491175.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33532 AN: 151844 Hom.: 4010 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.192 AC: 44676 AN: 232218 Hom.: 4628 Cov.: 0 AF XY: 0.191 AC XY: 22549 AN XY: 117886

African (AFR) AF: 0.258 AC: 1770 AN: 6864

American (AMR) AF: 0.292 AC: 2043 AN: 7006

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 2543 AN: 8906

East Asian (EAS) AF: 0.0497 AC: 1093 AN: 21972

South Asian (SAS) AF: 0.130 AC: 270 AN: 2076

European-Finnish (FIN) AF: 0.185 AC: 3519 AN: 19072

Middle Eastern (MID) AF: 0.212 AC: 258 AN: 1216

European-Non Finnish (NFE) AF: 0.201 AC: 30042 AN: 149638

Other (OTH) AF: 0.203 AC: 3138 AN: 15468

GnomAD4 genome AF: 0.221 AC: 33548 AN: 151962 Hom.: 4009 Cov.: 31 AF XY: 0.222 AC XY: 16476 AN XY: 74312

African (AFR) AF: 0.263 AC: 10897 AN: 41400

American (AMR) AF: 0.291 AC: 4439 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1060 AN: 3468

East Asian (EAS) AF: 0.0638 AC: 330 AN: 5170

South Asian (SAS) AF: 0.143 AC: 687 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1923 AN: 10580

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13614 AN: 67948

Other (OTH) AF: 0.206 AC: 433 AN: 2106

Alfa AF: 0.216 Hom.: 6226

Bravo AF: 0.234

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs6676862; hg19: chr1-159969008;