rs2493168

Positions:

• chr6-53253437-A-G
• chr6-53253437-A-T

Variant summary

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

The XR_007059612.1(LOC124901332):​n.1103-7825T>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 0.722 in 150,354 control chromosomes in the GnomAD database, including 40,914 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 0.72 (40914 hom., cov: 29)
• Consequence: LOC124901332 XR_007059612.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

LOC124901332 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901332	XR_007059612.1	n.1103-7825T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.721 AC: 108379 AN: 150242 Hom.: 40858 Cov.: 29

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.722 AC: 108493 AN: 150354 Hom.: 40914 Cov.: 29 AF XY: 0.710 AC XY: 52095 AN XY: 73412

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.746

Alfa AF: 0.678 Hom.: 4250

Bravo AF: 0.749

Asia WGS AF: 0.577 AC: 1940 AN: 3366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2493168; hg19: chr6-53118235;