rs8081154

chr17-50763678-T-A

Variant summary

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

The NM_001358683.3(ANKRD40CL):c.41-121A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 397,138 control chromosomes in the GnomAD database, including 47,155 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 (16051 hom., cov: 33)
  • Exomes 𝑓: 0.50 (31104 hom.)
• Consequence: ANKRD40CL NM_001358683.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

ANKRD40CL (HGNC:26080): (ANKRD40 C-terminal like)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD40CL	NM_001358683.3	c.41-121A>T		intron_variant		ENST00000450727.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD40CL	ENST00000450727.6	c.41-121A>T		intron_variant		3	NM_001358683.3	A2
ANKRD40CL	ENST00000502517.5	c.41-121A>T		intron_variant		1
ANKRD40CL	ENST00000643007.1	c.125-121A>T		intron_variant				P2
ANKRD40CL	ENST00000300458.1	n.2004A>T		non_coding_transcript_exon_variant	2/3	2

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67804 AN: 152052 Hom.: 16057 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.498 AC: 122013 AN: 244968 Hom.: 31104 Cov.: 0 AF XY: 0.499 AC XY: 62016 AN XY: 124232

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.444

Gnomad4 ASJ exome AF: 0.491

Gnomad4 EAS exome AF: 0.338

Gnomad4 SAS exome AF: 0.416

Gnomad4 FIN exome AF: 0.595

Gnomad4 NFE exome AF: 0.524

Gnomad4 OTH exome AF: 0.486

GnomAD4 genome AF: 0.446 AC: 67797 AN: 152170 Hom.: 16051 Cov.: 33 AF XY: 0.448 AC XY: 33287 AN XY: 74374

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.472

Alfa AF: 0.504 Hom.: 2429

Bravo AF: 0.429

Asia WGS AF: 0.398 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.2
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8081154; hg19: chr17-48841039;