rs4931243

chr12-30028454-G-C

Variant summary

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

The XR_931474.1(LOC105369715):n.135-14524C>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 0.379 in 151,884 control chromosomes in the GnomAD database, including 11,590 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 0.38 (11590 hom., cov: 32)
• Consequence: LOC105369715 XR_931474.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751

Genes affected

LOC105369715 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369715	XR_931474.1	n.135-14524C>G		intron_variant, non_coding_transcript_variant
LOC105369715	XR_001749060.1	n.135-14524C>G		intron_variant, non_coding_transcript_variant
LOC105369715	XR_001749061.1	n.135-14524C>G		intron_variant, non_coding_transcript_variant
LOC105369715	XR_931476.1	n.135-14524C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57527 AN: 151766 Hom.: 11593 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.379 AC: 57541 AN: 151884 Hom.: 11590 Cov.: 32 AF XY: 0.376 AC XY: 27925 AN XY: 74214

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.414

Alfa AF: 0.409 Hom.: 1644

Bravo AF: 0.367

Asia WGS AF: 0.342 AC: 1191 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.44
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4931243; hg19: chr12-30181387;