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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000597698.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARPC1AP2	ENST00000597698.1	TSL:6	n.922C>A		non_coding_transcript_exon	Exon 1 of 1
	ZNF702P	ENST00000594516.1	TSL:4	n.160-18115G>T		intron	N/A
	ZNF702P	ENST00000600425.6	TSL:3	n.130-18115G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1650937;

hg19: chr19-53508214;

COSMIC: COSV74082671;