chr9-34645685-CT-C

Position:

• chr9-34645685-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The variant allele was found at a frequency of 0.00571 in 137,498 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.0057 (5 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-CT-C is Benign according to our data. Variant chr9-34645685-CT-C is described in ClinVar as [Benign]. Clinvar id is 1698652.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00571 (785/137498) while in subpopulation AFR AF= 0.0167 (614/36710). AF 95% confidence interval is 0.0156. There are 5 homozygotes in gnomad4. There are 377 alleles in male gnomad4 subpopulation. Median coverage is 27. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34645686delT		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00567 AC: 780 AN: 137492 Hom.: 5 Cov.: 27

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00320

Gnomad ASJ AF: 0.000306

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.00163

Gnomad FIN AF: 0.00506

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000925

Gnomad OTH AF: 0.00380

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

GnomAD4 genome AF: 0.00571 AC: 785 AN: 137498 Hom.: 5 Cov.: 27 AF XY: 0.00569 AC XY: 377 AN XY: 66298

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.00320

Gnomad4 ASJ AF: 0.000306

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.00163

Gnomad4 FIN AF: 0.00506

Gnomad4 NFE AF: 0.000925

Gnomad4 OTH AF: 0.00431

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

Jun 29, 2022

Variant summary: GALT c.-1004delT is located in the untranscribed region upstream of the GALT gene region. The variant allele was found at a frequency of 0.0088 in 23774 control chromosomes (gnomAD). The observed variant frequency is approximately 3 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.-1004delT 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;