rs878998

chr6-41112262-C-T

Variant summary

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

The NR_026938.2(ADCY10P1):n.1584+906C>T 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 0.0961 in 152,172 control chromosomes in the GnomAD database, including 740 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 0.096 (740 hom., cov: 32)
• Consequence: ADCY10P1 NR_026938.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

ADCY10P1 (HGNC:44143): (ADCY10 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCY10P1	NR_026938.2	n.1584+906C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCY10P1	ENST00000457653.8	n.1004+941C>T		intron_variant, non_coding_transcript_variant
ADCY10P1	ENST00000567255.2	n.1584+906C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14616 AN: 152054 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0961 AC: 14623 AN: 152172 Hom.: 740 Cov.: 32 AF XY: 0.0941 AC XY: 7004 AN XY: 74414

Gnomad4 AFR AF: 0.0884

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.104

Alfa AF: 0.112 Hom.: 135

Bravo AF: 0.0994

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878998; hg19: chr6-41080001;