rs764073

Variant names:

• chr12-16806210-G-A
• rs764073
• XR_931397.3:n.674-18163C>T

Variant summary

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

The XR_931397.3(LOC105369677):​n.674-18163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,008 control chromosomes in the GnomAD database, including 30,190 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 0.62 (30190 hom., cov: 32)
• Consequence: LOC105369677 XR_931397.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 1 publications found

Genes affected

LOC105369677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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: 0.624 AC: 94775 AN: 151890 Hom.: 30154 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.624 AC: 94856 AN: 152008 Hom.: 30190 Cov.: 32 AF XY: 0.621 AC XY: 46149 AN XY: 74298

African (AFR) AF: 0.747 AC: 30973 AN: 41482

American (AMR) AF: 0.498 AC: 7604 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2546 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2199 AN: 5154

South Asian (SAS) AF: 0.681 AC: 3281 AN: 4820

European-Finnish (FIN) AF: 0.587 AC: 6190 AN: 10540

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40046 AN: 67944

Other (OTH) AF: 0.638 AC: 1348 AN: 2114

Alfa AF: 0.622 Hom.: 3865

Bravo AF: 0.622

Asia WGS AF: 0.575 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.9
DANN	Benign	0.86
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs764073; hg19: chr12-16959144;