rs17431881

Variant names:

• chr2-221329199-G-C
• rs17431881
• ENST00000702411.2:n.376-40694C>G

Variant summary

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

The ENST00000702411.2(ENSG00000290000):​n.376-40694C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0768 in 152,070 control chromosomes in the GnomAD database, including 604 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 0.077 (604 hom., cov: 32)
• Consequence: ENSG00000290000 ENST00000702411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853
• Publications: 0 publications found

Genes affected

ENSG00000290000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702411.2. 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
	ENSG00000290000	ENST00000702411.2		n.376-40694C>G		intron	N/A
	ENSG00000290000	ENST00000798102.1		n.228+22087C>G		intron	N/A
	ENSG00000290000	ENST00000798103.1		n.90-40694C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0769 AC: 11686 AN: 151952 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0768 AC: 11686 AN: 152070 Hom.: 604 Cov.: 32 AF XY: 0.0743 AC XY: 5521 AN XY: 74310

African (AFR) AF: 0.0194 AC: 805 AN: 41514

American (AMR) AF: 0.0702 AC: 1070 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1148 AN: 10544

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7959 AN: 67990

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0921 Hom.: 86

Bravo AF: 0.0737

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.61
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs17431881; hg19: chr2-222193919;