rs7535475

chr1-161493797-C-Achr1-161493797-C-T

Variant summary

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

The XR_922214.3(LOC105371473):n.1903+178C>A 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 0.506 in 152,026 control chromosomes in the GnomAD database, including 20,216 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 0.51 (20216 hom., cov: 33)
• Consequence: LOC105371473 XR_922214.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

Genes affected

LOC105371473 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371473	XR_922214.3	n.1903+178C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76877 AN: 151908 Hom.: 20215 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.506 AC: 76918 AN: 152026 Hom.: 20216 Cov.: 33 AF XY: 0.501 AC XY: 37206 AN XY: 74336

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.524

Alfa AF: 0.451 Hom.: 2005

Bravo AF: 0.507

Asia WGS AF: 0.352 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7535475; hg19: chr1-161463587;