rs994960

Variant names:

• chr3-73682765-G-A
• rs994960
• XR_001740755.1:n.351-4340C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-73682765-G-A
• chr3-73682765-G-C
• chr3-73682765-G-T

Variant summary

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

The XR_001740755.1(LOC105377164):​n.351-4340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,948 control chromosomes in the GnomAD database, including 14,717 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 0.41 (14717 hom., cov: 31)
• Consequence: LOC105377164 XR_001740755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 4 publications found

Genes affected

LOC105377164 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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: 0.415 AC: 62994 AN: 151830 Hom.: 14711 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.415 AC: 63007 AN: 151948 Hom.: 14717 Cov.: 31 AF XY: 0.416 AC XY: 30912 AN XY: 74274

African (AFR) AF: 0.183 AC: 7570 AN: 41442

American (AMR) AF: 0.463 AC: 7062 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2878 AN: 5148

South Asian (SAS) AF: 0.492 AC: 2366 AN: 4806

European-Finnish (FIN) AF: 0.501 AC: 5279 AN: 10546

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34969 AN: 67962

Other (OTH) AF: 0.420 AC: 885 AN: 2106

Alfa AF: 0.345 Hom.: 1733

Bravo AF: 0.400

Asia WGS AF: 0.498 AC: 1731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.43
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs994960; hg19: chr3-73731916;