rs9510968

Variant names:

• chr13-23938264-A-G
• rs9510968
• ENST00000793729.1:n.741+3026T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-23938264-A-G
• chr13-23938264-A-T

Variant summary

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

The ENST00000793729.1(ENSG00000290660):​n.741+3026T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,932 control chromosomes in the GnomAD database, including 23,297 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 0.54 (23297 hom., cov: 32)
• Consequence: ENSG00000290660 ENST00000793729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 4 publications found

Genes affected

ENSG00000290660 (HGNC:):

ANKRD20A19P (HGNC:42737): (ankyrin repeat domain 20 family member A19, pseudogene)

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 (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD20A19P	NR_073430.1	n.3861+3026T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290660	ENST00000793729.1	n.741+3026T>C		intron_variant	Intron 4 of 5
ENSG00000290660	ENST00000793730.1	n.338+3026T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82039 AN: 151814 Hom.: 23298 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.540 AC: 82068 AN: 151932 Hom.: 23297 Cov.: 32 AF XY: 0.541 AC XY: 40144 AN XY: 74258

African (AFR) AF: 0.389 AC: 16113 AN: 41426

American (AMR) AF: 0.442 AC: 6754 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1805 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3657 AN: 5170

South Asian (SAS) AF: 0.625 AC: 3008 AN: 4816

European-Finnish (FIN) AF: 0.685 AC: 7208 AN: 10528

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41793 AN: 67950

Other (OTH) AF: 0.535 AC: 1129 AN: 2110

Alfa AF: 0.589 Hom.: 98377

Bravo AF: 0.516

Asia WGS AF: 0.620 AC: 2155 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	6.9
DANN	Benign	0.60
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9510968; hg19: chr13-24512403; COSMIC: COSV69739116;