9-34646057-AAG-A

Position:

• chr9-34646057-AAG-A

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 0.0283 in 149,316 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.028 (97 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0250

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-34646057-AAG-A is Benign according to our data. Variant chr9-34646057-AAG-A is described in ClinVar as [Benign]. Clinvar id is 1331459.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34646058_34646059delAG		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALT	ENST00000605275.1	n.209-619_209-618delAG		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 4226 AN: 149236 Hom.: 98 Cov.: 31

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0598

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0357

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

GnomAD4 genome AF: 0.0283 AC: 4224 AN: 149316 Hom.: 97 Cov.: 31 AF XY: 0.0296 AC XY: 2155 AN XY: 72806

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.0598

Gnomad4 EAS AF: 0.00156

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0461

Gnomad4 NFE AF: 0.0314

Gnomad4 OTH AF: 0.0354

Bravo AF: 0.0234

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 20, 2021

Variant summary: GALT c.-631_-630delAG is located in the untranscribed region upstream of the GALT gene region. The variant allele was found at a frequency of 0.027 in 28816 control chromosomes in the gnomAD database, including 10 homozygotes. The observed variant frequency is approximately 9.42 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. 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: rs149007102; hg19: chr9-34646054;