rs10879312

Positions:

• chr12-71680955-G-T

Variant summary

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

The XR_007063367.1(LOC124902965):​n.143+4967C>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 0.164 in 152,110 control chromosomes in the GnomAD database, including 3,041 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 0.16 (3041 hom., cov: 32)
• Consequence: LOC124902965 XR_007063367.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

Genes affected

LOC124902965 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902965	XR_007063367.1	n.143+4967C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24850 AN: 151992 Hom.: 3038 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.164 AC: 24880 AN: 152110 Hom.: 3041 Cov.: 32 AF XY: 0.161 AC XY: 11948 AN XY: 74390

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0982

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.144

Alfa AF: 0.109 Hom.: 1665

Bravo AF: 0.174

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.9
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10879312; hg19: chr12-72074735;