9-5610381-C-T

Variant names:

• chr9-5610381-C-T
• rs4740820
• XR_007061405.1:n.11101G>A

Variant summary

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

The XR_007061405.1(INCR1):​n.11101G>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 0.311 in 151,966 control chromosomes in the GnomAD database, including 7,914 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 0.31 (7914 hom., cov: 32)
• Consequence: INCR1 XR_007061405.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

INCR1 (HGNC:56906):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650674.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286162	ENST00000650674.2		n.226+18409G>A		intron	N/A
	ENSG00000286162	ENST00000661858.1		n.182+19186G>A		intron	N/A
	ENSG00000286162	ENST00000740229.1		n.214+19186G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47252 AN: 151848 Hom.: 7885 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.311 AC: 47318 AN: 151966 Hom.: 7914 Cov.: 32 AF XY: 0.316 AC XY: 23495 AN XY: 74256

African (AFR) AF: 0.303 AC: 12563 AN: 41420

American (AMR) AF: 0.417 AC: 6359 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3472

East Asian (EAS) AF: 0.630 AC: 3251 AN: 5158

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4816

European-Finnish (FIN) AF: 0.230 AC: 2427 AN: 10536

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18302 AN: 67992

Other (OTH) AF: 0.298 AC: 629 AN: 2108

Alfa AF: 0.295 Hom.: 20870

Bravo AF: 0.327

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs4740820; hg19: chr9-5610381; COSMIC: COSV60324296;