rs2996336

Variant names:

• chr9-38579063-G-A
• rs2996336
• NM_147195.4:c.2248-915C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_147195.4(ANKRD18A):​c.2248-915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 152,180 control chromosomes in the GnomAD database, including 33 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 0.011 (33 hom., cov: 32)
• Consequence: ANKRD18A NM_147195.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 0 publications found

Genes affected

ANKRD18A (HGNC:23643): (ankyrin repeat domain 18A)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0112 (1709/152180) while in subpopulation AFR AF = 0.0388 (1611/41494). AF 95% confidence interval is 0.0372. There are 33 homozygotes in GnomAd4. There are 798 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD18A	NM_147195.4	c.2248-915C>T		intron_variant	Intron 12 of 15	ENST00000399703.6	NP_671728.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD18A	ENST00000399703.6	c.2248-915C>T		intron_variant	Intron 12 of 15	1	NM_147195.4	ENSP00000382610.4
ANKRD18A	ENST00000602295.5	c.418-915C>T		intron_variant	Intron 4 of 7	1		ENSP00000473463.1
ANKRD18A	ENST00000703205.1	c.2434-915C>T		intron_variant	Intron 14 of 17			ENSP00000515234.1
ANKRD18A	ENST00000703204.1	n.*1208-915C>T		intron_variant	Intron 9 of 16			ENSP00000515233.1

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 1701 AN: 152062 Hom.: 33 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00471

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00574

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0112 AC: 1709 AN: 152180 Hom.: 33 Cov.: 32 AF XY: 0.0107 AC XY: 798 AN XY: 74400

African (AFR) AF: 0.0388 AC: 1611 AN: 41494

American (AMR) AF: 0.00477 AC: 73 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.000416 AC: 2 AN: 4804

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 68002

Other (OTH) AF: 0.00568 AC: 12 AN: 2112

Alfa AF: 0.00763 Hom.: 1

Bravo AF: 0.0128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.34
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2996336; hg19: chr9-38579060;