rs7486905

Positions:

• chr12-106766391-G-A

Variant summary

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

The NR_040246.1(LOC100287944):​n.142+8299C>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 0.385 in 151,872 control chromosomes in the GnomAD database, including 11,488 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 0.39 (11488 hom., cov: 31)
• Consequence: LOC100287944 NR_040246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287944	NR_040246.1	n.142+8299C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000551505.4	n.229+8299C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000549203.2	n.142+8299C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000652234.1	n.237+8299C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58453 AN: 151754 Hom.: 11468 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.385 AC: 58510 AN: 151872 Hom.: 11488 Cov.: 31 AF XY: 0.381 AC XY: 28299 AN XY: 74220

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.375

Alfa AF: 0.376 Hom.: 1388

Bravo AF: 0.399

Asia WGS AF: 0.336 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7486905; hg19: chr12-107160169;