rs663646

Variant names:

• chr5-78989955-G-A
• rs663646

Your query was ambiguous. Multiple possible variants found:

• chr5-78989955-G-A
• chr5-78989955-G-T

Variant summary

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

The variant allele was found at a frequency of 0.627 in 152,080 control chromosomes in the GnomAD database, including 31,795 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 (31795 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.73 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: 0.628 AC: 95386 AN: 151962 Hom.: 31790 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.627 AC: 95414 AN: 152080 Hom.: 31795 Cov.: 33 AF XY: 0.628 AC XY: 46715 AN XY: 74366

African (AFR) AF: 0.402 AC: 16655 AN: 41448

American (AMR) AF: 0.741 AC: 11337 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2289 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2420 AN: 5178

South Asian (SAS) AF: 0.552 AC: 2658 AN: 4816

European-Finnish (FIN) AF: 0.811 AC: 8573 AN: 10572

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.723 AC: 49184 AN: 67986

Other (OTH) AF: 0.633 AC: 1337 AN: 2112

Alfa AF: 0.666 Hom.: 4484

Bravo AF: 0.614

Asia WGS AF: 0.540 AC: 1880 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.96
DANN	Benign	0.88
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs663646; hg19: chr5-78285778;