9-34645685-C-CTT

Position:

• chr9-34645685-C-CTT

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 0.0276 in 137,514 control chromosomes in the GnomAD database, including 215 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.028 (215 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-CTT is Benign according to our data. Variant chr9-34645685-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1677034.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34645685_34645686insTT		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0276 AC: 3791 AN: 137508 Hom.: 215 Cov.: 27

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0127

Gnomad ASJ AF: 0.00275

Gnomad EAS AF: 0.000417

Gnomad SAS AF: 0.00256

Gnomad FIN AF: 0.00114

Gnomad MID AF: 0.00699

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0223

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

GnomAD4 genome AF: 0.0276 AC: 3796 AN: 137514 Hom.: 215 Cov.: 27 AF XY: 0.0266 AC XY: 1765 AN XY: 66306

Gnomad4 AFR AF: 0.0947

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.00275

Gnomad4 EAS AF: 0.000418

Gnomad4 SAS AF: 0.00257

Gnomad4 FIN AF: 0.00114

Gnomad4 NFE AF: 0.00113

Gnomad4 OTH AF: 0.0221

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

Mar 08, 2022

Variant summary: GALT c.-1005_-1004dupTT is located in the untranscribed region upstream of the GALT gene region. The variant allele was found at a frequency of 0.028 in 23774 control chromosomes, predominantly at a frequency of 0.09 within the African or African-American subpopulation in the gnomAD database, including 44 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 31.18 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.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;