rs35963845

Variant names:

• chr10-45678880-G-A
• rs35963845
• ENST00000454844.1:n.189G>A

Variant summary

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

The ENST00000454844.1(AGAP10P):​n.189G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 1,596,984 control chromosomes in the GnomAD database, including 48,468 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 0.22 (4033 hom., cov: 31)
  • Exomes 𝑓: 0.24 (44435 hom.)
• Consequence: AGAP10P ENST00000454844.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 7 publications found

Genes affected

AGAP10P (HGNC:23659): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 10, pseudogene)

ENSG00000299671 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGAP10P	NR_160521.1	n.365G>A		non_coding_transcript_exon_variant	Exon 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGAP10P	ENST00000454844.1	n.189G>A		non_coding_transcript_exon_variant	Exon 1 of 7	6
ENSG00000299671	ENST00000765542.1	n.510G>A		non_coding_transcript_exon_variant	Exon 1 of 5
ENSG00000299671	ENST00000765543.1	n.29G>A		non_coding_transcript_exon_variant	Exon 1 of 8

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33934 AN: 151560 Hom.: 4024 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.244 AC: 352421 AN: 1445310 Hom.: 44435 Cov.: 151 AF XY: 0.249 AC XY: 179059 AN XY: 719406

African (AFR) AF: 0.189 AC: 6305 AN: 33396

American (AMR) AF: 0.166 AC: 7420 AN: 44704

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 7754 AN: 26128

East Asian (EAS) AF: 0.236 AC: 9373 AN: 39696

South Asian (SAS) AF: 0.368 AC: 31730 AN: 86148

European-Finnish (FIN) AF: 0.199 AC: 7825 AN: 39278

Middle Eastern (MID) AF: 0.275 AC: 1253 AN: 4562

European-Non Finnish (NFE) AF: 0.239 AC: 266105 AN: 1111252

Other (OTH) AF: 0.244 AC: 14656 AN: 60146

GnomAD4 genome AF: 0.224 AC: 33951 AN: 151674 Hom.: 4033 Cov.: 31 AF XY: 0.226 AC XY: 16755 AN XY: 74150

African (AFR) AF: 0.186 AC: 7666 AN: 41172

American (AMR) AF: 0.193 AC: 2949 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1070 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1199 AN: 5142

South Asian (SAS) AF: 0.371 AC: 1789 AN: 4816

European-Finnish (FIN) AF: 0.192 AC: 2033 AN: 10566

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16455 AN: 67914

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.221 Hom.: 495

Bravo AF: 0.220

Asia WGS AF: 0.291 AC: 1009 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs35963845; hg19: chr10-46174328;