rs1343444

Positions:

• chr6-48587331-C-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 0.152 in 151,738 control chromosomes in the GnomAD database, including 2,700 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 0.15 (2700 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48587331C>G		intergenic_region
LOC107986602	XR_001744151.1	n.467-9854C>G		intron_variant
LOC107986602	XR_001744152.1	n.235-9854C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22990 AN: 151620 Hom.: 2679 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.152 AC: 23036 AN: 151738 Hom.: 2700 Cov.: 32 AF XY: 0.155 AC XY: 11518 AN XY: 74178

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.0699

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.157

Alfa AF: 0.122 Hom.: 226

Bravo AF: 0.177

Asia WGS AF: 0.340 AC: 1179 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343444; hg19: chr6-48555067;