chr1-225918985-G-T

Variant names:

• chr1-225918985-G-T
• rs360064
• ENST00000432920.2:c.575+2223C>A

Variant summary

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

The ENST00000432920.2(ENSG00000255835):​c.575+2223C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,110 control chromosomes in the GnomAD database, including 1,431 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 0.13 (1431 hom., cov: 31)
• Consequence: ENSG00000255835 ENST00000432920.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 12 publications found

Genes affected

ENSG00000255835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255835	ENST00000432920.2	c.575+2223C>A		intron_variant	Intron 5 of 7	2		ENSP00000414068.2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19457 AN: 151992 Hom.: 1431 Cov.: 31

Gnomad AFR AF: 0.0685

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.128 AC: 19457 AN: 152110 Hom.: 1431 Cov.: 31 AF XY: 0.128 AC XY: 9489 AN XY: 74352

African (AFR) AF: 0.0685 AC: 2845 AN: 41532

American (AMR) AF: 0.133 AC: 2038 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.0469 AC: 242 AN: 5158

South Asian (SAS) AF: 0.161 AC: 775 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1386 AN: 10580

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11097 AN: 67980

Other (OTH) AF: 0.140 AC: 294 AN: 2100

Alfa AF: 0.0377 Hom.: 81

Bravo AF: 0.123

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.29

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: rs360064; hg19: chr1-226106685;