rs722442

Positions:

• chr6-41121942-A-G
• chr6-41121942-A-T

Variant summary

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

The NR_026938.2(ADCY10P1):​n.2743A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,078 control chromosomes in the GnomAD database, including 17,228 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 0.45 (17228 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADCY10P1 NR_026938.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY10P1	NR_026938.2	n.2743A>G		splice_region_variant, non_coding_transcript_exon_variant	14/23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCY10P1	ENST00000567255.2	n.2743A>G		splice_region_variant, non_coding_transcript_exon_variant	14/23	1
ADCY10P1	ENST00000457653.8	n.2122-1035A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68109 AN: 151962 Hom.: 17186 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.423

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.448 AC: 68204 AN: 152078 Hom.: 17228 Cov.: 32 AF XY: 0.446 AC XY: 33153 AN XY: 74350

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.419

Alfa AF: 0.360 Hom.: 13603

Bravo AF: 0.469

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
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: rs722442; hg19: chr6-41089681;