rs7593687

Positions:

• chr2-34474248-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0758 in 133,852 control chromosomes in the GnomAD database, including 1,700 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.076 (1700 hom., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34474248C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01320	ENST00000422558.1	n.475+89679C>T		intron_variant		4
LINC01320	ENST00000650021.1	n.219+89679C>T		intron_variant
LINC01320	ENST00000654103.1	n.532-2316C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 10141 AN: 133740 Hom.: 1698 Cov.: 23

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.00233

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000680

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0219

Gnomad NFE AF: 0.00153

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0758 AC: 10152 AN: 133852 Hom.: 1700 Cov.: 23 AF XY: 0.0737 AC XY: 4795 AN XY: 65074

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.00233

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000455

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00153

Gnomad4 OTH AF: 0.0593

Alfa AF: 0.0594 Hom.: 123

Asia WGS AF: 0.0110 AC: 39 AN: 3378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.96
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7593687; hg19: chr2-34699315;