rs12662871

Positions:

• chr6-14429331-T-C

Variant summary

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

The XR_926510.3(LOC105374942):​n.636-2317A>G 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 0.187 in 151,910 control chromosomes in the GnomAD database, including 2,732 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 0.19 (2732 hom., cov: 32)
• Consequence: LOC105374942 XR_926510.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

Genes affected

LOC105374942 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374942	XR_926510.3	n.636-2317A>G		intron_variant, non_coding_transcript_variant
LOC105374942	XR_007059468.1	n.3166A>G		non_coding_transcript_exon_variant	4/4
LOC105374942	XR_007059469.1	n.4722A>G		non_coding_transcript_exon_variant	5/5
LOC105374942	XR_926511.3	n.636-2317A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28362 AN: 151792 Hom.: 2730 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.187 AC: 28389 AN: 151910 Hom.: 2732 Cov.: 32 AF XY: 0.184 AC XY: 13661 AN XY: 74234

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.179

Alfa AF: 0.174 Hom.: 4858

Bravo AF: 0.185

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12662871; hg19: chr6-14429562;