rs2524005

Positions:

• chr6-29931900-G-A
• chr6-29931900-G-T

Variant summary

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

The XR_007059541.1(LOC124901298):​n.814-3163C>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 0.18 in 146,910 control chromosomes in the GnomAD database, including 2,918 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 (2918 hom., cov: 27)
• Consequence: LOC124901298 XR_007059541.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

Genes affected

LOC124901298 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901298	XR_007059541.1	n.814-3163C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.180 AC: 26480 AN: 146796 Hom.: 2909 Cov.: 27

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 26504 AN: 146910 Hom.: 2918 Cov.: 27 AF XY: 0.177 AC XY: 12654 AN XY: 71664

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.175

Alfa AF: 0.190 Hom.: 3611

Asia WGS AF: 0.189 AC: 658 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524005; hg19: chr6-29899677;