rs2909580

chr7-81547488-T-C

Variant summary

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

The NR_136264.1(LOC105369146):n.474+12632A>G 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 0.272 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: LOC105369146 NR_136264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105369146	NR_136264.1	n.474+12632A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDHR17P	ENST00000636004.1	n.2184+12632A>G		intron_variant, non_coding_transcript_variant
	ENST00000636281.1	n.805+12632A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000412900.3	n.589+12632A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0701

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.310

Alfa AF: 0.357 Hom.: 13272

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2909580; hg19: chr7-81176804;