rs10456499

Positions:

• chr6-41115613-G-A
• chr6-41115613-G-C

Variant summary

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

The NR_026938.2(ADCY10P1):​n.1585-1685G>A 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 0.693 in 152,022 control chromosomes in the GnomAD database, including 38,015 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 0.69 (38015 hom., cov: 30)
• Consequence: ADCY10P1 NR_026938.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCY10P1	NR_026938.2	n.1585-1685G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCY10P1	ENST00000457653.8	n.1005-1685G>A		intron_variant, non_coding_transcript_variant
ADCY10P1	ENST00000567255.2	n.1585-1685G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105191 AN: 151904 Hom.: 37953 Cov.: 30

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.693 AC: 105313 AN: 152022 Hom.: 38015 Cov.: 30 AF XY: 0.691 AC XY: 51290 AN XY: 74276

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.673

Alfa AF: 0.606 Hom.: 39365

Bravo AF: 0.707

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.96
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10456499; hg19: chr6-41083352;