1-220428281-C-T

Variant names:

• chr1-220428281-C-T
• rs7512221
• ENST00000718956.1:n.231+527C>T

Variant summary

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

The ENST00000718956.1(ENSG00000293784):​n.231+527C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,222 control chromosomes in the GnomAD database, including 55,839 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 0.84 (55839 hom., cov: 32)
• Consequence: ENSG00000293784 ENST00000718956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 7 publications found

Genes affected

ENSG00000293784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718956.1. 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
	ENSG00000293784	ENST00000718956.1		n.231+527C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128175 AN: 152104 Hom.: 55821 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.843 AC: 128249 AN: 152222 Hom.: 55839 Cov.: 32 AF XY: 0.846 AC XY: 62945 AN XY: 74436

African (AFR) AF: 0.596 AC: 24705 AN: 41474

American (AMR) AF: 0.924 AC: 14135 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3101 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4652 AN: 5186

South Asian (SAS) AF: 0.865 AC: 4180 AN: 4830

European-Finnish (FIN) AF: 0.965 AC: 10247 AN: 10616

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64301 AN: 68040

Other (OTH) AF: 0.877 AC: 1852 AN: 2112

Alfa AF: 0.907 Hom.: 200794

Bravo AF: 0.829

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.4
DANN	Benign	0.70
PhyloP100		0.17

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: rs7512221;

hg19: chr1-220601623;