3-124205956-T-G

Position:

• chr3-124205956-T-G

Variant summary

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

The NM_001388419.1(KALRN):​c.74-22034T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,028 control chromosomes in the GnomAD database, including 51,002 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 0.81 (51002 hom., cov: 31)
• Consequence: KALRN NM_001388419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KALRN	NM_001388419.1	c.74-22034T>G		intron_variant		ENST00000682506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KALRN	ENST00000682506.1	c.74-22034T>G		intron_variant			NM_001388419.1	A2

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123319 AN: 151910 Hom.: 50980 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.812 AC: 123387 AN: 152028 Hom.: 51002 Cov.: 31 AF XY: 0.805 AC XY: 59805 AN XY: 74326

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.817

Alfa AF: 0.872 Hom.: 30044

Bravo AF: 0.802

Asia WGS AF: 0.671 AC: 2337 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	12
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1444767; hg19: chr3-123924803;