9-34645848-A-ATTTTTTT

Position:

• chr9-34645848-A-ATTTTTTT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.00079 (4 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.901

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 9-34645848-A-ATTTTTTT is Benign according to our data. Variant chr9-34645848-A-ATTTTTTT is described in ClinVar as [Benign]. Clinvar id is 1343439.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34645848_34645849insTTTTTTT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALT	ENST00000605275.1	n.209-829_209-828insTTTTTTT		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.000796 AC: 100 AN: 125634 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.00137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000492

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000236

Gnomad SAS AF: 0.0109

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00388

Gnomad NFE AF: 0.000114

Gnomad OTH AF: 0.000589

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

GnomAD4 genome AF: 0.000788 AC: 99 AN: 125612 Hom.: 4 Cov.: 0 AF XY: 0.000924 AC XY: 55 AN XY: 59556

Gnomad4 AFR AF: 0.00137

Gnomad4 AMR AF: 0.000491

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000236

Gnomad4 SAS AF: 0.0107

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000114

Gnomad4 OTH AF: 0.000585

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

Feb 22, 2022

Variant summary: GALT c.-843_-837dupTTTTTTT is located in the untranscribed region upstream of the GALT gene region. The variant allele was found at a frequency of 0.00079 in 124530 control chromosomes in the gnomAD database (v3.1.2 dataset), including 4 homozygotes. The variant is predominantly found within the South Asian subpopulation at a frequency of 0.011. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 4-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 a benign polymorphism. To our knowledge, no occurrence of c.-843_-837dupTTTTTTT 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: rs549043849; hg19: chr9-34645845;