rs2909580

Variant names:

• chr7-81547488-T-C
• rs2909580
• ENST00000412900.3:n.589+12632A>G

Variant summary

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

The ENST00000412900.3(ENSG00000293394):​n.589+12632A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,122 control chromosomes in the GnomAD database, including 6,970 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 0.27 (6970 hom., cov: 32)
• Consequence: ENSG00000293394 ENST00000412900.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 3 publications found

Genes affected

ENSG00000293394 (HGNC:):

CDHR17P (HGNC:53741): (cadherin related family member 17, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369146	NR_136264.1	n.474+12632A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293394	ENST00000412900.3	n.589+12632A>G		intron_variant	Intron 4 of 4	5
CDHR17P	ENST00000636004.1	n.2184+12632A>G		intron_variant	Intron 16 of 20	6
ENSG00000293394	ENST00000636281.1	n.805+12632A>G		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41414 AN: 152002 Hom.: 6972 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.272 AC: 41408 AN: 152122 Hom.: 6970 Cov.: 32 AF XY: 0.274 AC XY: 20338 AN XY: 74350

African (AFR) AF: 0.0701 AC: 2914 AN: 41552

American (AMR) AF: 0.305 AC: 4666 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.155 AC: 804 AN: 5180

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4824

European-Finnish (FIN) AF: 0.363 AC: 3831 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25008 AN: 67942

Other (OTH) AF: 0.310 AC: 655 AN: 2114

Alfa AF: 0.335 Hom.: 16540

Bravo AF: 0.260

Asia WGS AF: 0.243 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.82
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs2909580; hg19: chr7-81176804;