7-81661206-A-G

Variant names:

• chr7-81661206-A-G
• rs7799610
• ENST00000413944.3:n.78+30123T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000413944.3(CDHR17P):​n.78+30123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,018 control chromosomes in the GnomAD database, including 51,070 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 0.81 (51070 hom., cov: 31)
• Consequence: CDHR17P ENST00000413944.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

Genes affected

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

LOC100128317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128317	NR_126025.1	n.78+30123T>C		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR17P	ENST00000413944.3	n.78+30123T>C		intron_variant	Intron 1 of 10	1
CDHR17P	ENST00000636281.1	n.228+29059T>C		intron_variant	Intron 1 of 7	5
CDHR17P	ENST00000648981.1	n.150+29059T>C		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122653 AN: 151900 Hom.: 51060 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.807 AC: 122698 AN: 152018 Hom.: 51070 Cov.: 31 AF XY: 0.805 AC XY: 59841 AN XY: 74310

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.838

Alfa AF: 0.896 Hom.: 79869

Bravo AF: 0.795

Asia WGS AF: 0.643 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	13
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7799610; hg19: chr7-81290522;