1-193520039-C-T

Variant names:

• chr1-193520039-C-T
• rs7554157
• ENST00000656143.2:n.153+46663C>T

Variant summary

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

The ENST00000656143.2(ENSG00000227240):​n.153+46663C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,992 control chromosomes in the GnomAD database, including 27,640 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 0.59 (27640 hom., cov: 31)
• Consequence: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656143.2. 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
	ENSG00000227240	ENST00000656143.2		n.153+46663C>T		intron	N/A
	ENSG00000286285	ENST00000691564.2		n.283-26009C>T		intron	N/A
	ENSG00000286285	ENST00000767304.1		n.346-26009C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90201 AN: 151874 Hom.: 27613 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.594 AC: 90271 AN: 151992 Hom.: 27640 Cov.: 31 AF XY: 0.588 AC XY: 43662 AN XY: 74264

African (AFR) AF: 0.621 AC: 25762 AN: 41474

American (AMR) AF: 0.522 AC: 7966 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3472

East Asian (EAS) AF: 0.192 AC: 988 AN: 5148

South Asian (SAS) AF: 0.435 AC: 2098 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6711 AN: 10550

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42234 AN: 67964

Other (OTH) AF: 0.593 AC: 1252 AN: 2112

Alfa AF: 0.591 Hom.: 12324

Bravo AF: 0.581

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.078
DANN	Benign	0.51
PhyloP100		-1.9

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: rs7554157;

hg19: chr1-193489169;