rs7628219

Variant names:

• chr3-70577209-C-T
• rs7628219
• XR_001740559.2:n.367-1256G>A

Variant summary

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

The XR_001740559.2(LOC105377152):​n.367-1256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 151,680 control chromosomes in the GnomAD database, including 1,967 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 0.15 (1967 hom., cov: 32)
• Consequence: LOC105377152 XR_001740559.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 6 publications found

Genes affected

LOC105377152 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22986 AN: 151560 Hom.: 1969 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.152 AC: 22995 AN: 151680 Hom.: 1967 Cov.: 32 AF XY: 0.148 AC XY: 10990 AN XY: 74112

African (AFR) AF: 0.182 AC: 7525 AN: 41322

American (AMR) AF: 0.200 AC: 3041 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3464

East Asian (EAS) AF: 0.0281 AC: 145 AN: 5158

South Asian (SAS) AF: 0.0685 AC: 329 AN: 4806

European-Finnish (FIN) AF: 0.119 AC: 1247 AN: 10522

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9866 AN: 67894

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.145 Hom.: 4450

Bravo AF: 0.159

Asia WGS AF: 0.0680 AC: 238 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.48
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs7628219; hg19: chr3-70626360;