1-228955828-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373143	XR_949234.2	n.142-7035G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;