chr6-41122943-C-T

Variant names:

• chr6-41122943-C-T
• rs6926079
• ENST00000567255.2:n.2745-34C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567255.2(ADCY10P1):​n.2745-34C>T variant causes a intron 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 ENST00000567255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 13 publications found

Genes affected

ADCY10P1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567255.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	NR_026938.2		n.2745-34C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	ENST00000567255.2	TSL:1	n.2745-34C>T		intron	N/A
	ADCY10P1	ENST00000457653.8	TSL:6	n.2122-34C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0904 AC: 34 AN: 376

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0190 AC: 788 AN: 41538

American (AMR) AF: 0.0780 AC: 1193 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0295 AC: 142 AN: 4820

European-Finnish (FIN) AF: 0.0839 AC: 887 AN: 10566

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7428 AN: 67984

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.0976 Hom.: 459

Bravo AF: 0.0723

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.31
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6926079; hg19: chr6-41090682;