rs6926079

Positions:

• chr6-41122943-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.2745-34C>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 0.0741 in 152,546 control chromosomes in the GnomAD database, including 551 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 (550 hom., cov: 32)
  • Exomes 𝑓: 0.092 (1 hom.)
• Consequence: ADCY10P1 NR_026938.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

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 = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY10P1	NR_026938.2	n.2745-34C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCY10P1	ENST00000457653.8	n.2122-34C>T		intron_variant, non_coding_transcript_variant
ADCY10P1	ENST00000567255.2	n.2745-34C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11263 AN: 152046 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0895

GnomAD4 exome AF: 0.0916 AC: 35 AN: 382 Hom.: 1 Cov.: 0 AF XY: 0.103 AC XY: 24 AN XY: 234

Gnomad4 FIN exome AF: 0.0904

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0740 AC: 11265 AN: 152164 Hom.: 550 Cov.: 32 AF XY: 0.0727 AC XY: 5405 AN XY: 74394

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0295

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0976 Hom.: 419

Bravo AF: 0.0723

Asia WGS AF: 0.0160 AC: 57 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	1.3
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: rs6926079; hg19: chr6-41090682;