rs1650937

Variant names:

• chr19-53004961-C-A
• rs1650937
• ENST00000597698.1:n.922C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-53004961-C-A
• chr19-53004961-C-T

Variant summary

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

The ENST00000597698.1(ARPC1AP2):​n.922C>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 0.125 in 1,434,494 control chromosomes in the GnomAD database, including 23,589 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 0.25 (9128 hom., cov: 32)
  • Exomes 𝑓: 0.11 (14461 hom.)
• Consequence: ARPC1AP2 ENST00000597698.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 1 publications found

Genes affected

ARPC1AP2 (HGNC:56495): (ARPC1A pseudogene 2)

ZNF702P (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARPC1AP2		n.53004961C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARPC1AP2	ENST00000597698.1	n.922C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ZNF702P	ENST00000594516.1	n.160-18115G>T		intron_variant	Intron 1 of 3	4
ZNF702P	ENST00000600425.6	n.130-18115G>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38699 AN: 152068 Hom.: 9111 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.226

GnomAD4 exome AF: 0.109 AC: 139956 AN: 1282306 Hom.: 14461 Cov.: 24 AF XY: 0.107 AC XY: 69008 AN XY: 646324

African (AFR) AF: 0.631 AC: 18848 AN: 29850

American (AMR) AF: 0.192 AC: 8495 AN: 44298

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 2889 AN: 25054

East Asian (EAS) AF: 0.395 AC: 15316 AN: 38756

South Asian (SAS) AF: 0.104 AC: 8577 AN: 82610

European-Finnish (FIN) AF: 0.0739 AC: 3924 AN: 53084

Middle Eastern (MID) AF: 0.124 AC: 669 AN: 5414

European-Non Finnish (NFE) AF: 0.0778 AC: 73847 AN: 948772

Other (OTH) AF: 0.136 AC: 7391 AN: 54468

GnomAD4 genome AF: 0.255 AC: 38765 AN: 152188 Hom.: 9128 Cov.: 32 AF XY: 0.253 AC XY: 18823 AN XY: 74400

African (AFR) AF: 0.613 AC: 25424 AN: 41476

American (AMR) AF: 0.209 AC: 3192 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2214 AN: 5182

South Asian (SAS) AF: 0.116 AC: 562 AN: 4828

European-Finnish (FIN) AF: 0.0700 AC: 742 AN: 10604

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0825 AC: 5610 AN: 68028

Other (OTH) AF: 0.226 AC: 478 AN: 2116

Alfa AF: 0.0564 Hom.: 66

Bravo AF: 0.281

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1650937; hg19: chr19-53508214; COSMIC: COSV74082671;