rs2596560

Positions:

• chr6-31387541-T-C
• chr6-31387541-T-G

Variant summary

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

The XR_007059542.1(LOC124901300):​n.160+193T>C 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 0.216 in 152,170 control chromosomes in the GnomAD database, including 3,635 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 0.22 (3635 hom., cov: 33)
• Consequence: LOC124901300 XR_007059542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

Genes affected

LOC124901300 (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 (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901300	XR_007059542.1	n.160+193T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32897 AN: 152052 Hom.: 3635 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.216 AC: 32913 AN: 152170 Hom.: 3635 Cov.: 33 AF XY: 0.217 AC XY: 16141 AN XY: 74416

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.200

Alfa AF: 0.216 Hom.: 2344

Bravo AF: 0.210

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2596560; hg19: chr6-31355318;