rs1343726

Positions:

• chr3-124148247-T-A
• chr3-124148247-T-C

Variant summary

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

The NM_001388419.1(KALRN):​c.74-79743T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,916 control chromosomes in the GnomAD database, including 6,409 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 0.28 (6409 hom., cov: 32)
• Consequence: KALRN NM_001388419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

KALRN (HGNC:4814): (kalirin RhoGEF kinase) Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein that interacts with the huntingtin-associated protein 1, which is a huntingtin binding protein that may function in vesicle trafficking. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KALRN	NM_001388419.1	c.74-79743T>A		intron_variant		ENST00000682506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KALRN	ENST00000682506.1	c.74-79743T>A		intron_variant			NM_001388419.1	A2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42154 AN: 151798 Hom.: 6410 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.278 AC: 42164 AN: 151916 Hom.: 6409 Cov.: 32 AF XY: 0.285 AC XY: 21120 AN XY: 74220

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.306

Alfa AF: 0.278 Hom.: 772

Bravo AF: 0.271

Asia WGS AF: 0.413 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343726; hg19: chr3-123867094;