rs6865651

Variant names:

• chr5-113915999-C-T
• rs6865651
• XR_007058906.1:n.2086-82177C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058906.1(LOC124901047):​n.2086-82177C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 1 publications found

Genes affected

LOC124901047 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.102 AC: 4245 AN: 41504

American (AMR) AF: 0.171 AC: 2618 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3470

East Asian (EAS) AF: 0.141 AC: 729 AN: 5178

South Asian (SAS) AF: 0.227 AC: 1098 AN: 4830

European-Finnish (FIN) AF: 0.296 AC: 3131 AN: 10562

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14587 AN: 67960

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.193 Hom.: 475

Bravo AF: 0.169

Asia WGS AF: 0.185 AC: 640 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.12

Splicing

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

Other links and lift over

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