14-87941372-TAA-TA

Position:

• chr14-87941372-TAA-TA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The ENST00000261304.7(GALC):​c.1834+22del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00046 (0 hom., cov: 0)
  • Exomes 𝑓: 0.033 (2 hom.)
• Consequence: GALC ENST00000261304.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

GALC (HGNC:4115): (galactosylceramidase) This gene encodes a lysosomal protein which hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Mutations in this gene have been associated with Krabbe disease, also known as globoid cell leukodystrophy. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 14-87941372-TA-T is Benign according to our data. Variant chr14-87941372-TA-T is described in Lovd as [Benign].
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALC	NM_000153.4	c.1834+22del		intron_variant		ENST00000261304.7	NP_000144.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALC	ENST00000261304.7	c.1834+22del		intron_variant		1	NM_000153.4	ENSP00000261304	P1

Frequencies

GnomAD3 genomes AF: 0.000463 AC: 68 AN: 146848 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000504

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000814

Gnomad ASJ AF: 0.000583

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000428

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.000225

Gnomad OTH AF: 0.000500

GnomAD4 exome AF: 0.0327 AC: 35355 AN: 1080020 Hom.: 2 Cov.: 16 AF XY: 0.0321 AC XY: 17529 AN XY: 546218

Gnomad4 AFR exome AF: 0.0758

Gnomad4 AMR exome AF: 0.0196

Gnomad4 ASJ exome AF: 0.0355

Gnomad4 EAS exome AF: 0.00725

Gnomad4 SAS exome AF: 0.0251

Gnomad4 FIN exome AF: 0.0299

Gnomad4 NFE exome AF: 0.0340

Gnomad4 OTH exome AF: 0.0333

GnomAD4 genome AF: 0.000463 AC: 68 AN: 146896 Hom.: 0 Cov.: 0 AF XY: 0.000393 AC XY: 28 AN XY: 71260

Gnomad4 AFR AF: 0.000502

Gnomad4 AMR AF: 0.000813

Gnomad4 ASJ AF: 0.000583

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000430

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.000225

Gnomad4 OTH AF: 0.000497

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs34752717; hg19: chr14-88407716;