rs1456222

Variant names:

• chr3-66934149-A-G
• rs1456222
• ENST00000777942.1:n.70+38196T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-66934149-A-G
• chr3-66934149-A-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+38196T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,020 control chromosomes in the GnomAD database, including 31,534 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 0.63 (31534 hom., cov: 32)
• Consequence: ENSG00000288039 ENST00000777942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377144	XR_940939.2	n.74+38196T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288039	ENST00000777942.1	n.70+38196T>C		intron_variant	Intron 1 of 3
ENSG00000288039	ENST00000777943.1	n.65+38196T>C		intron_variant	Intron 1 of 3
ENSG00000288039	ENST00000777944.1	n.46+38196T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95139 AN: 151902 Hom.: 31503 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.626 AC: 95202 AN: 152020 Hom.: 31534 Cov.: 32 AF XY: 0.630 AC XY: 46808 AN XY: 74306

African (AFR) AF: 0.400 AC: 16557 AN: 41434

American (AMR) AF: 0.673 AC: 10273 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4971 AN: 5174

South Asian (SAS) AF: 0.846 AC: 4078 AN: 4820

European-Finnish (FIN) AF: 0.648 AC: 6841 AN: 10564

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48198 AN: 67976

Other (OTH) AF: 0.623 AC: 1316 AN: 2112

Alfa AF: 0.667 Hom.: 11820

Bravo AF: 0.613

Asia WGS AF: 0.835 AC: 2904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.64
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1456222; hg19: chr3-66984573;