rs12176541

chr6-48562562-G-Achr6-48562562-G-T

Variant summary

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

The XR_001744151.1(LOC107986602):n.466+23281G>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 0.0847 in 152,144 control chromosomes in the GnomAD database, including 1,610 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 0.085 (1610 hom., cov: 32)
• Consequence: LOC107986602 XR_001744151.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

Genes affected

LOC107986602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986602	XR_001744151.1	n.466+23281G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12856 AN: 152026 Hom.: 1592 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0847 AC: 12889 AN: 152144 Hom.: 1610 Cov.: 32 AF XY: 0.0908 AC XY: 6756 AN XY: 74374

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.0550

Gnomad4 OTH AF: 0.0933

Alfa AF: 0.0650 Hom.: 1332

Bravo AF: 0.102

Asia WGS AF: 0.308 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12176541; hg19: chr6-48530298;