1-119366891-A-G

Variant names:

• chr1-119366891-A-G
• rs3753264
• ENST00000840373.1:n.99-2672T>C

Variant summary

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

The ENST00000840373.1(ENSG00000227712):​n.99-2672T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,090 control chromosomes in the GnomAD database, including 19,217 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 0.46 (19217 hom., cov: 32)
• Consequence: ENSG00000227712 ENST00000840373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 6 publications found

Genes affected

ENSG00000227712 (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 (AFR) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840373.1. 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
	ENSG00000227712	ENST00000840373.1		n.99-2672T>C		intron	N/A
	ENSG00000227712	ENST00000840376.1		n.118-6197T>C		intron	N/A
	ENSG00000227712	ENST00000840377.1		n.97-6197T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70389 AN: 151972 Hom.: 19175 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.463 AC: 70490 AN: 152090 Hom.: 19217 Cov.: 32 AF XY: 0.465 AC XY: 34570 AN XY: 74332

African (AFR) AF: 0.758 AC: 31432 AN: 41470

American (AMR) AF: 0.365 AC: 5585 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3466

East Asian (EAS) AF: 0.540 AC: 2792 AN: 5166

South Asian (SAS) AF: 0.526 AC: 2536 AN: 4818

European-Finnish (FIN) AF: 0.350 AC: 3699 AN: 10578

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22115 AN: 67978

Other (OTH) AF: 0.434 AC: 915 AN: 2110

Alfa AF: 0.388 Hom.: 25411

Bravo AF: 0.474

Asia WGS AF: 0.560 AC: 1948 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.72
PhyloP100		0.47

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: rs3753264;

hg19: chr1-119909514;