1-222098425-C-T

Variant names:

• chr1-222098425-C-T
• rs873549
• ENST00000416510.1:n.279-8860G>A

Variant summary

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

The ENST00000416510.1(ENSG00000236230):​n.279-8860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,192 control chromosomes in the GnomAD database, including 42,258 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 0.74 (42258 hom., cov: 33)
• Consequence: ENSG00000236230 ENST00000416510.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 33 publications found

Genes affected

ENSG00000236230 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416510.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236230	ENST00000416510.1	TSL:1	n.279-8860G>A		intron	N/A
	ENSG00000236230	ENST00000652067.1		n.706-8860G>A		intron	N/A
	ENSG00000236230	ENST00000738770.1		n.178-8860G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112900 AN: 152074 Hom.: 42225 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.742 AC: 112978 AN: 152192 Hom.: 42258 Cov.: 33 AF XY: 0.743 AC XY: 55285 AN XY: 74398

African (AFR) AF: 0.818 AC: 33998 AN: 41542

American (AMR) AF: 0.712 AC: 10876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2459 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3397 AN: 5166

South Asian (SAS) AF: 0.589 AC: 2839 AN: 4824

European-Finnish (FIN) AF: 0.744 AC: 7873 AN: 10576

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.723 AC: 49169 AN: 68016

Other (OTH) AF: 0.721 AC: 1522 AN: 2112

Alfa AF: 0.722 Hom.: 137873

Bravo AF: 0.742

Asia WGS AF: 0.579 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		0.034

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs873549;

hg19: chr1-222271767;