ENST00000656143.2:n.200+92514G>A

Variant names:

• chr1-193765770-G-A
• rs2025934
• ENST00000656143.2:n.200+92514G>A

Variant summary

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

The ENST00000656143.2(ENSG00000227240):​n.200+92514G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 151,966 control chromosomes in the GnomAD database, including 101 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 0.032 (101 hom., cov: 31)
• Consequence: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 3 publications found

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5235-120551G>A		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2	n.200+92514G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4813 AN: 151848 Hom.: 101 Cov.: 31

Gnomad AFR AF: 0.00929

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0253

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0316 AC: 4809 AN: 151966 Hom.: 101 Cov.: 31 AF XY: 0.0300 AC XY: 2232 AN XY: 74280

African (AFR) AF: 0.00927 AC: 384 AN: 41440

American (AMR) AF: 0.0212 AC: 323 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4812

European-Finnish (FIN) AF: 0.0304 AC: 321 AN: 10548

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3500 AN: 67970

Other (OTH) AF: 0.0280 AC: 59 AN: 2106

Alfa AF: 0.0449 Hom.: 534

Bravo AF: 0.0292

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.58
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2025934; hg19: chr1-193734900;