NM_001358683.3:c.41-121A>T

Variant names:

• chr17-50763678-T-A
• rs8081154
• NM_001358683.3:c.41-121A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ANKRD40CL	NM_001358683.3	c.41-121A>T		intron_variant	Intron 2 of 3	ENST00000450727.6	NP_001345612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD40CL	ENST00000450727.6	c.41-121A>T		intron_variant	Intron 2 of 3	3	NM_001358683.3	ENSP00000494384.1
ANKRD40CL	ENST00000502517.5	c.41-121A>T		intron_variant	Intron 2 of 2	1		ENSP00000493576.1
ANKRD40CL	ENST00000300458.1	n.2004A>T		non_coding_transcript_exon_variant	Exon 2 of 3	2
ANKRD40CL	ENST00000643007.1	c.125-121A>T		intron_variant	Intron 2 of 3			ENSP00000496239.1

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

African (AFR) AF: 0.283 AC: 2025 AN: 7164

American (AMR) AF: 0.444 AC: 3285 AN: 7406

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 4520 AN: 9210

East Asian (EAS) AF: 0.338 AC: 7719 AN: 22834

South Asian (SAS) AF: 0.416 AC: 910 AN: 2188

European-Finnish (FIN) AF: 0.595 AC: 12525 AN: 21052

Middle Eastern (MID) AF: 0.479 AC: 619 AN: 1292

European-Non Finnish (NFE) AF: 0.524 AC: 82481 AN: 157506

Other (OTH) AF: 0.486 AC: 7929 AN: 16316

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

African (AFR) AF: 0.280 AC: 11627 AN: 41528

American (AMR) AF: 0.451 AC: 6890 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1694 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1873 AN: 5174

South Asian (SAS) AF: 0.424 AC: 2047 AN: 4830

European-Finnish (FIN) AF: 0.586 AC: 6193 AN: 10570

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35906 AN: 67992

Other (OTH) AF: 0.472 AC: 997 AN: 2114

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs8081154; hg19: chr17-48841039;