rs12418451

Positions:

• chr11-69167951-G-A

Variant summary

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

The NR_104161.1(LOC338694):​n.475+378C>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 0.219 in 151,952 control chromosomes in the GnomAD database, including 4,364 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 0.22 (4364 hom., cov: 31)
• Consequence: LOC338694 NR_104161.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

Genes affected

(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 = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC338694	NR_104161.1	n.475+378C>T		intron_variant, non_coding_transcript_variant
LOC105369366	XR_950255.3	n.108+1043G>A		intron_variant, non_coding_transcript_variant
LOC105369366	XR_950256.3	n.108+1043G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000562772.1	n.477+378C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33283 AN: 151834 Hom.: 4365 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0383

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.219 AC: 33288 AN: 151952 Hom.: 4364 Cov.: 31 AF XY: 0.217 AC XY: 16102 AN XY: 74256

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0382

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.255

Alfa AF: 0.257 Hom.: 756

Bravo AF: 0.210

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12418451; hg19: chr11-68935419;