rs1456227

Variant names:

• chr3-66954132-C-A
• rs1456227
• ENST00000777942.1:n.70+18213G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-66954132-C-A
• chr3-66954132-C-G
• chr3-66954132-C-T

Variant summary

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

The ENST00000777942.1(ENSG00000288039):​n.70+18213G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,038 control chromosomes in the GnomAD database, including 44,939 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 0.77 (44939 hom., cov: 32)
• Consequence: ENSG00000288039 ENST00000777942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 2 publications found

Genes affected

ENSG00000288039 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377144	XR_940939.2	n.74+18213G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288039	ENST00000777942.1	n.70+18213G>T		intron_variant	Intron 1 of 3
ENSG00000288039	ENST00000777943.1	n.65+18213G>T		intron_variant	Intron 1 of 3
ENSG00000288039	ENST00000777944.1	n.46+18213G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116290 AN: 151920 Hom.: 44896 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.766 AC: 116389 AN: 152038 Hom.: 44939 Cov.: 32 AF XY: 0.769 AC XY: 57153 AN XY: 74306

African (AFR) AF: 0.680 AC: 28191 AN: 41466

American (AMR) AF: 0.817 AC: 12465 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2430 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4974 AN: 5174

South Asian (SAS) AF: 0.918 AC: 4429 AN: 4822

European-Finnish (FIN) AF: 0.777 AC: 8217 AN: 10578

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53214 AN: 67958

Other (OTH) AF: 0.758 AC: 1599 AN: 2110

Alfa AF: 0.744 Hom.: 5229

Bravo AF: 0.762

Asia WGS AF: 0.889 AC: 3091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1456227; hg19: chr3-67004556;