rs1035496

chr5-41138147-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742650.2(LOC105374739):n.887-23166T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

Genes affected

LOC105374739 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374739	XR_001742650.2	n.887-23166T>C		intron_variant, non_coding_transcript_variant
LOC105374739	XR_001742651.2	n.297-23166T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.211

Alfa AF: 0.209 Hom.: 1730

Bravo AF: 0.194

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	16
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1035496; hg19: chr5-41138249;