rs4964469

Positions:

• chr12-106556209-G-A
• chr12-106556209-G-C

Variant summary

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

The NR_040246.1(LOC100287944):​n.143-48399C>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 0.451 in 151,858 control chromosomes in the GnomAD database, including 16,240 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 0.45 (16240 hom., cov: 32)
• Consequence: LOC100287944 NR_040246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

(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 = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287944	NR_040246.1	n.143-48399C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000551505.4	n.230-56027C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000549203.2	n.143-48399C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68473 AN: 151740 Hom.: 16225 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.451 AC: 68521 AN: 151858 Hom.: 16240 Cov.: 32 AF XY: 0.451 AC XY: 33438 AN XY: 74172

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.404

Alfa AF: 0.386 Hom.: 25504

Bravo AF: 0.443

Asia WGS AF: 0.418 AC: 1455 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	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4964469; hg19: chr12-106949987;