rs4711652

Positions:

• chr6-40885000-G-A
• chr6-40885000-G-C
• chr6-40885000-G-T

Variant summary

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

The NR_110873.1(LOC101929555):​n.595-1897C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,020 control chromosomes in the GnomAD database, including 19,718 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 0.50 (19718 hom., cov: 32)
• Consequence: LOC101929555 NR_110873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

Genes affected

LOC101929555 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929555	NR_110873.1	n.595-1897C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75579 AN: 151902 Hom.: 19711 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.497 AC: 75605 AN: 152020 Hom.: 19718 Cov.: 32 AF XY: 0.501 AC XY: 37201 AN XY: 74304

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.524

Alfa AF: 0.551 Hom.: 46202

Bravo AF: 0.489

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711652; hg19: chr6-40852739;