rs7311298

chr12-115518350-T-C

Variant summary

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

The XR_945389.3(LOC105370003):n.119-9936A>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 0.16 in 152,210 control chromosomes in the GnomAD database, including 4,012 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 (4012 hom., cov: 33)
• Consequence: LOC105370003 XR_945389.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

Genes affected

LOC105370003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370003	XR_945389.3	n.119-9936A>G		intron_variant, non_coding_transcript_variant
LOC105370003	XR_945388.3	n.119-9936A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24243 AN: 152092 Hom.: 3993 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.160 AC: 24311 AN: 152210 Hom.: 4012 Cov.: 33 AF XY: 0.155 AC XY: 11555 AN XY: 74434

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.0877

Gnomad4 ASJ AF: 0.0776

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0664 Hom.: 1036

Bravo AF: 0.175

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.24
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7311298; hg19: chr12-115956155;