chr9-34645848-A-ATT

Position:

• chr9-34645848-A-ATT

Variant summary

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

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

• Frequency: Genomes: 𝑓 0.065 (385 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 Benign. Variant got -10 ACMG points.

• BP6: Variant 9-34645848-A-ATT is Benign according to our data. Variant chr9-34645848-A-ATT is described in ClinVar as [Benign]. Clinvar id is 1331397.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34645848_34645849insTT		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0648 AC: 8138 AN: 125558 Hom.: 383 Cov.: 0

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.00825

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0504

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0495

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

GnomAD4 genome AF: 0.0649 AC: 8147 AN: 125538 Hom.: 385 Cov.: 0 AF XY: 0.0641 AC XY: 3818 AN XY: 59522

Gnomad4 AFR AF: 0.0814

Gnomad4 AMR AF: 0.0533

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.00828

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0627

Gnomad4 OTH AF: 0.0498

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 14, 2021

Variant summary: GALT c.-838_-837dupTT is located in the untranscribed region upstream of the GALT gene region. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.063 in 19482 control chromosomes, predominantly at a frequency of 0.08 within the African or African-American subpopulation in the gnomAD database, including 23 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 28 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 found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.-838_-837dupTT 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;