chr2-163461366-T-C

Variant names:

• chr2-163461366-T-C
• rs12476047
• ENST00000809663.1:n.376+8025T>C

Variant summary

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

The ENST00000809663.1(ENSG00000305215):​n.376+8025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,054 control chromosomes in the GnomAD database, including 5,179 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 0.25 (5179 hom., cov: 32)
• Consequence: ENSG00000305215 ENST00000809663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 11 publications found

Genes affected

ENSG00000305215 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305215	ENST00000809663.1	n.376+8025T>C		intron_variant	Intron 2 of 3
ENSG00000305215	ENST00000809664.1	n.375+8025T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37950 AN: 151934 Hom.: 5175 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.250 AC: 37988 AN: 152054 Hom.: 5179 Cov.: 32 AF XY: 0.249 AC XY: 18484 AN XY: 74324

African (AFR) AF: 0.146 AC: 6072 AN: 41494

American (AMR) AF: 0.366 AC: 5586 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3466

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5164

South Asian (SAS) AF: 0.147 AC: 708 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2719 AN: 10574

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19653 AN: 67954

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.283 Hom.: 23873

Bravo AF: 0.262

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12476047; hg19: chr2-164317876;