ENST00000661858.1:n.277-31335G>A

Variant names:

• chr9-5490522-C-T
• rs944141
• ENST00000661858.1:n.277-31335G>A

Variant summary

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

The ENST00000661858.1(ENSG00000286162):​n.277-31335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,098 control chromosomes in the GnomAD database, including 5,618 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 0.26 (5618 hom., cov: 32)
• Consequence: ENSG00000286162 ENST00000661858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 7 publications found

Genes affected

ENSG00000286162 (HGNC:56906):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INCR1	XR_007061406.1	n.256-31335G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286162	ENST00000661858.1	n.277-31335G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40083 AN: 151980 Hom.: 5609 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.264 AC: 40117 AN: 152098 Hom.: 5618 Cov.: 32 AF XY: 0.265 AC XY: 19728 AN XY: 74374

African (AFR) AF: 0.311 AC: 12919 AN: 41478

American (AMR) AF: 0.328 AC: 5019 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3470

East Asian (EAS) AF: 0.173 AC: 895 AN: 5182

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2541 AN: 10570

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15672 AN: 67974

Other (OTH) AF: 0.265 AC: 560 AN: 2114

Alfa AF: 0.242 Hom.: 3971

Bravo AF: 0.274

Asia WGS AF: 0.279 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs944141; hg19: chr9-5490522;