1-118274106-C-T

Variant names:

• chr1-118274106-C-T
• rs7527203
• ENST00000807785.1:n.383+19570G>A

Variant summary

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

The ENST00000807785.1(ENSG00000305021):​n.383+19570G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,244 control chromosomes in the GnomAD database, including 106 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 0.035 (106 hom., cov: 33)
• Consequence: ENSG00000305021 ENST00000807785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 4 publications found

Genes affected

ENSG00000305021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807785.1. 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
	ENSG00000305021	ENST00000807785.1		n.383+19570G>A		intron	N/A
	ENSG00000305021	ENST00000807786.1		n.159+19570G>A		intron	N/A
	ENSG00000305021	ENST00000807787.1		n.216+5662G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0346 AC: 5257 AN: 152126 Hom.: 105 Cov.: 33

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0554

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0346 AC: 5264 AN: 152244 Hom.: 106 Cov.: 33 AF XY: 0.0335 AC XY: 2497 AN XY: 74452

African (AFR) AF: 0.0525 AC: 2183 AN: 41552

American (AMR) AF: 0.0175 AC: 268 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3468

East Asian (EAS) AF: 0.0144 AC: 75 AN: 5192

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4818

European-Finnish (FIN) AF: 0.0250 AC: 265 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0302 AC: 2050 AN: 67990

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0314 Hom.: 221

Bravo AF: 0.0341

Asia WGS AF: 0.0370 AC: 131 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.2
DANN	Benign	0.81
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7527203; hg19: chr1-118816729;