9-34646343-G-T

Position:

• chr9-34646343-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.0279 in 152,312 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Genomes: 𝑓 0.028 (101 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.171

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 9-34646343-G-T is Benign according to our data. Variant chr9-34646343-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1196736.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34646343G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALT	ENST00000605275.1	n.209-334G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0279 AC: 4253 AN: 152194 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0279 AC: 4251 AN: 152312 Hom.: 101 Cov.: 32 AF XY: 0.0292 AC XY: 2178 AN XY: 74486

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0427

Gnomad4 NFE AF: 0.0309

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0279 Hom.: 8

Bravo AF: 0.0234

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12551313; hg19: chr9-34646340;