rs7486905

Variant names:

• chr12-106766391-G-A
• rs7486905
• ENST00000549203.2:n.142+8299C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000549203.2(ENSG00000257545):​n.142+8299C>T variant causes a intron 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: ENSG00000257545 ENST00000549203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 2 publications found

Genes affected

ENSG00000257545 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC100287944	NR_040246.1	n.142+8299C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257545	ENST00000549203.2	n.142+8299C>T		intron_variant	Intron 1 of 3	4
ENSG00000257545	ENST00000551505.4	n.229+8299C>T		intron_variant	Intron 1 of 2	4
ENSG00000257545	ENST00000652234.1	n.237+8299C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.456 AC: 18864 AN: 41390

American (AMR) AF: 0.363 AC: 5546 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3470

East Asian (EAS) AF: 0.329 AC: 1692 AN: 5142

South Asian (SAS) AF: 0.401 AC: 1928 AN: 4804

European-Finnish (FIN) AF: 0.281 AC: 2972 AN: 10568

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24658 AN: 67910

Other (OTH) AF: 0.375 AC: 793 AN: 2112

Alfa AF: 0.377 Hom.: 1465

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
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7486905; hg19: chr12-107160169;