rs4747887

Positions:

• chr10-6135719-T-C

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 0.43 in 151,932 control chromosomes in the GnomAD database, including 14,212 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 0.43 (14212 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6135719T>C		intergenic_region
LOC101928080	XR_930619.3	n.614+5299A>G		intron_variant
LOC101928080	XR_930620.3	n.614+5299A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65339 AN: 151814 Hom.: 14200 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.430 AC: 65393 AN: 151932 Hom.: 14212 Cov.: 32 AF XY: 0.428 AC XY: 31780 AN XY: 74248

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.474

Alfa AF: 0.457 Hom.: 21332

Bravo AF: 0.437

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
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: rs4747887; hg19: chr10-6177682;