10-97218485-G-T

Variant names:

• chr10-97218485-G-T
• rs1271003
• ENST00000479633.2:n.1474+10662C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000479633.2(ARHGAP19-SLIT1):​n.1474+10662C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00019 (0 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: ARHGAP19-SLIT1 ENST00000479633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 0 publications found

Genes affected

ARHGAP19-SLIT1 (HGNC:48348): (ARHGAP19-SLIT1 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring Rho GTPase activating protein 19 (ARHGAP19) and slit homolog 1 (SLIT1) genes on chromosome 10. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000479633.2. 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
	ARHGAP19-SLIT1	NR_037909.1		n.1520+10662C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP19-SLIT1	ENST00000479633.2	TSL:2	n.1474+10662C>A		intron	N/A	ENSP00000473567.1

Frequencies

GnomAD3 genomes AF: 0.000207 AC: 17 AN: 82296 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.000366

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000291

Gnomad ASJ AF: 0.000405

Gnomad EAS AF: 0.000336

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000677

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000919

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000194 AC: 16 AN: 82334 Hom.: 0 Cov.: 20 AF XY: 0.000184 AC XY: 7 AN XY: 38058

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000313 AC: 6 AN: 19166

American (AMR) AF: 0.000291 AC: 2 AN: 6884

Ashkenazi Jewish (ASJ) AF: 0.000405 AC: 1 AN: 2472

East Asian (EAS) AF: 0.000338 AC: 1 AN: 2960

South Asian (SAS) AF: 0.00 AC: 0 AN: 2522

European-Finnish (FIN) AF: 0.000677 AC: 2 AN: 2954

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 122

European-Non Finnish (NFE) AF: 0.0000919 AC: 4 AN: 43540

Other (OTH) AF: 0.00 AC: 0 AN: 1056

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.3
DANN	Benign	0.89
PhyloP100		-1.5

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: rs1271003; hg19: chr10-98978242;