9-34645685-C-CT

Position:

• chr9-34645685-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The variant allele was found at a frequency of 0.111 in 137,474 control chromosomes in the GnomAD database, including 992 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (992 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.520

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-34645685-C-CT is Benign according to our data. Variant chr9-34645685-C-CT is described in ClinVar as [Benign]. Clinvar id is 1331423.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34645685_34645686insT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALT	ENST00000605275.1	n.209-992_209-991insT		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 15258 AN: 137468 Hom.: 994 Cov.: 27

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.111 AC: 15257 AN: 137474 Hom.: 992 Cov.: 27 AF XY: 0.110 AC XY: 7265 AN XY: 66292

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.105

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Dec 16, 2021

Variant summary: GALT c.-1004dupT is located in the untranscribed region upstream of the GALT gene. The variant allele was found at a frequency of 0.1 in 23774 control chromosomes in the gnomAD database, including 156 homozygotes. The observed variant frequency is approximately 36-fold of the estimated maximal expected allele frequency for a pathogenic variant in GALT causing Galactosemia phenotype (0.0029), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.-1004dupT in individuals affected with Galactosemia and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201344398; hg19: chr9-34645682;