rs1035496

Variant names:

• chr5-41138147-T-C
• rs1035496
• XR_001742650.2:n.887-23166T>C

Variant summary

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

The XR_001742650.2(LOC105374739):​n.887-23166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,170 control chromosomes in the GnomAD database, including 3,093 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 0.19 (3093 hom., cov: 32)
• Consequence: LOC105374739 XR_001742650.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 1 publications found

Genes affected

LOC105374739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.187 AC: 28400 AN: 152052 Hom.: 3090 Cov.: 32

Gnomad AFR AF: 0.0948

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.187 AC: 28418 AN: 152170 Hom.: 3093 Cov.: 32 AF XY: 0.188 AC XY: 13996 AN XY: 74408

African (AFR) AF: 0.0945 AC: 3925 AN: 41534

American (AMR) AF: 0.285 AC: 4344 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3466

East Asian (EAS) AF: 0.294 AC: 1518 AN: 5166

South Asian (SAS) AF: 0.331 AC: 1597 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10604

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14022 AN: 67990

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.207 Hom.: 1906

Bravo AF: 0.194

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1035496; hg19: chr5-41138249;