rs528957

Variant names:

• chr7-141069659-T-C
• rs528957
• XR_928053.4:n.207-257T>C

Variant summary

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

The XR_928053.4(LOC105375537):​n.207-257T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,122 control chromosomes in the GnomAD database, including 55,396 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 0.85 (55396 hom., cov: 31)
• Consequence: LOC105375537 XR_928053.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 6 publications found

Genes affected

LOC105375537 (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 (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129028 AN: 152006 Hom.: 55368 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.849 AC: 129105 AN: 152122 Hom.: 55396 Cov.: 31 AF XY: 0.851 AC XY: 63255 AN XY: 74366

African (AFR) AF: 0.710 AC: 29421 AN: 41442

American (AMR) AF: 0.895 AC: 13684 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4706 AN: 5166

South Asian (SAS) AF: 0.850 AC: 4088 AN: 4812

European-Finnish (FIN) AF: 0.937 AC: 9937 AN: 10600

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61348 AN: 68024

Other (OTH) AF: 0.864 AC: 1825 AN: 2112

Alfa AF: 0.885 Hom.: 250469

Bravo AF: 0.840

Asia WGS AF: 0.885 AC: 3077 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	1.6
DANN	Benign	0.64
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs528957; hg19: chr7-140769459;