rs7649861

Variant names:

• chr3-144451858-G-A
• rs7649861
• XR_001740941.2:n.20091-16228G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-144451858-G-A
• chr3-144451858-G-C

Variant summary

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

The XR_924558.4(LOC105374140):​n.254-16228G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,008 control chromosomes in the GnomAD database, including 31,297 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 (31297 hom., cov: 32)
• Consequence: LOC105374140 XR_924558.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 1 publications found

Genes affected

LOC105374140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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: 0.634 AC: 96357 AN: 151890 Hom.: 31272 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.670

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.634 AC: 96430 AN: 152008 Hom.: 31297 Cov.: 32 AF XY: 0.630 AC XY: 46820 AN XY: 74286

African (AFR) AF: 0.754 AC: 31269 AN: 41478

American (AMR) AF: 0.578 AC: 8839 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1604 AN: 5164

South Asian (SAS) AF: 0.679 AC: 3268 AN: 4816

European-Finnish (FIN) AF: 0.588 AC: 6201 AN: 10538

Middle Eastern (MID) AF: 0.686 AC: 199 AN: 290

European-Non Finnish (NFE) AF: 0.601 AC: 40817 AN: 67954

Other (OTH) AF: 0.640 AC: 1352 AN: 2112

Alfa AF: 0.626 Hom.: 15322

Bravo AF: 0.636

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.44
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7649861; hg19: chr3-144170700;