rs12449606

chr17-70152670-C-A

Variant summary

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

The XR_934953.3(LOC105371882):n.330-1677G>T 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 0.212 in 152,108 control chromosomes in the GnomAD database, including 4,965 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 0.21 (4965 hom., cov: 32)
• Consequence: LOC105371882 XR_934953.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

LOC105371882 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371882	XR_934953.3	n.330-1677G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32143 AN: 151990 Hom.: 4947 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.212 AC: 32208 AN: 152108 Hom.: 4965 Cov.: 32 AF XY: 0.209 AC XY: 15574 AN XY: 74376

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.192

Alfa AF: 0.139 Hom.: 1944

Bravo AF: 0.233

Asia WGS AF: 0.145 AC: 505 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.2
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12449606; hg19: chr17-68148811;