rs778373

Variant names:

• chr1-228955828-G-T
• rs778373
• XR_949234.2:n.142-7035G>T

Variant summary

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

The XR_949234.2(LOC105373143):​n.142-7035G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,118 control chromosomes in the GnomAD database, including 5,818 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 0.25 (5818 hom., cov: 32)
• Consequence: LOC105373143 XR_949234.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878
• Publications: 2 publications found

Genes affected

LOC105373143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 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: 0.251 AC: 38188 AN: 152000 Hom.: 5816 Cov.: 32

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.251 AC: 38202 AN: 152118 Hom.: 5818 Cov.: 32 AF XY: 0.256 AC XY: 19027 AN XY: 74346

African (AFR) AF: 0.0747 AC: 3104 AN: 41534

American (AMR) AF: 0.250 AC: 3819 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1612 AN: 5148

South Asian (SAS) AF: 0.446 AC: 2148 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3471 AN: 10550

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.322 AC: 21902 AN: 67992

Other (OTH) AF: 0.281 AC: 593 AN: 2114

Alfa AF: 0.299 Hom.: 19610

Bravo AF: 0.236

Asia WGS AF: 0.347 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs778373; hg19: chr1-229091575; COSMIC: COSV60036678;