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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777942.1. 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
	ENSG00000288039	ENST00000777942.1		n.70+38196T>C		intron	N/A
	ENSG00000288039	ENST00000777943.1		n.65+38196T>C		intron	N/A
	ENSG00000288039	ENST00000777944.1		n.46+38196T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1456222;

hg19: chr3-66984573;