rs6865651

Positions:

• chr5-113915999-C-T

Variant summary

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

The XR_007058906.1(LOC124901047):​n.2086-82177C>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 0.182 in 152,096 control chromosomes in the GnomAD database, including 2,804 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 0.18 (2804 hom., cov: 32)
• Consequence: LOC124901047 XR_007058906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

Genes affected

LOC124901047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901047	XR_007058906.1	n.2086-82177C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27680 AN: 151978 Hom.: 2805 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.182 AC: 27683 AN: 152096 Hom.: 2804 Cov.: 32 AF XY: 0.186 AC XY: 13847 AN XY: 74352

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.164

Alfa AF: 0.196 Hom.: 472

Bravo AF: 0.169

Asia WGS AF: 0.185 AC: 640 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6865651; hg19: chr5-113251696; COSMIC: COSV60183802;