rs11968153

chr6-41121571-G-A

Variant summary

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

The NR_026938.2(ADCY10P1):n.2586+97G>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 0.0741 in 152,518 control chromosomes in the GnomAD database, including 549 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 0.074 (547 hom., cov: 32)
  • Exomes 𝑓: 0.10 (2 hom.)
• Consequence: ADCY10P1 NR_026938.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCY10P1	NR_026938.2	n.2586+97G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCY10P1	ENST00000457653.8	n.2121+832G>A		intron_variant, non_coding_transcript_variant
ADCY10P1	ENST00000567255.2	n.2586+97G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11259 AN: 151994 Hom.: 547 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0899

GnomAD4 exome AF: 0.101 AC: 41 AN: 406 Hom.: 2 AF XY: 0.104 AC XY: 26 AN XY: 250

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0740 AC: 11261 AN: 152112 Hom.: 547 Cov.: 32 AF XY: 0.0725 AC XY: 5394 AN XY: 74362

Gnomad4 AFR AF: 0.0192

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0841

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0988 Hom.: 106

Bravo AF: 0.0724

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	13
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11968153; hg19: chr6-41089310;