rs2025267

chr6-4158288-G-A

Variant summary

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

The XR_007059416.1(LOC124901246):n.999+12619G>A 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 0.814 in 152,190 control chromosomes in the GnomAD database, including 50,984 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 0.81 (50984 hom., cov: 32)
• Consequence: LOC124901246 XR_007059416.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712

Genes affected

LOC124901246 (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 (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901246	XR_007059416.1	n.999+12619G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123864 AN: 152074 Hom.: 50955 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.814 AC: 123951 AN: 152190 Hom.: 50984 Cov.: 32 AF XY: 0.817 AC XY: 60806 AN XY: 74390

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.808

Alfa AF: 0.770 Hom.: 60279

Bravo AF: 0.817

Asia WGS AF: 0.876 AC: 3049 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	0.037
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025267; hg19: chr6-4158522;