rs13198118

Positions:

• chr6-30802955-T-G

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 0.175 in 151,968 control chromosomes in the GnomAD database, including 3,014 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 0.17 (3014 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30802955T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000419357.6	n.146-4183A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26492 AN: 151850 Hom.: 3009 Cov.: 30

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.175 AC: 26521 AN: 151968 Hom.: 3014 Cov.: 30 AF XY: 0.182 AC XY: 13518 AN XY: 74262

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.203

Alfa AF: 0.175 Hom.: 4418

Bravo AF: 0.183

Asia WGS AF: 0.393 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13198118; hg19: chr6-30770732;