rs7551414

Variant names:

• chr1-232856544-T-A
• rs7551414
• ENST00000667494.2:n.225-1758T>A

Variant summary

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

The ENST00000667494.2(ENSG00000286774):​n.225-1758T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 152,318 control chromosomes in the GnomAD database, including 37 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 0.015 (37 hom., cov: 33)
• Consequence: ENSG00000286774 ENST00000667494.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503
• Publications: 0 publications found

Genes affected

ENSG00000286774 (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 (EAS) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667494.2. 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
	ENSG00000286774	ENST00000667494.2		n.225-1758T>A		intron	N/A
	ENSG00000286774	ENST00000833157.1		n.210-1758T>A		intron	N/A
	ENSG00000286774	ENST00000833158.1		n.210-1758T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2244 AN: 152200 Hom.: 37 Cov.: 33

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00811

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00275

Gnomad OTH AF: 0.0119

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

GnomAD4 genome AF: 0.0148 AC: 2251 AN: 152318 Hom.: 37 Cov.: 33 AF XY: 0.0156 AC XY: 1165 AN XY: 74496

African (AFR) AF: 0.0268 AC: 1116 AN: 41580

American (AMR) AF: 0.00810 AC: 124 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.0774 AC: 401 AN: 5182

South Asian (SAS) AF: 0.0709 AC: 342 AN: 4824

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10622

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00275 AC: 187 AN: 68014

Other (OTH) AF: 0.0113 AC: 24 AN: 2116

Alfa AF: 0.00656 Hom.: 2

Bravo AF: 0.0140

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		0.50

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: rs7551414;

hg19: chr1-232992290;