rs1905471

Positions:

• chr13-63437530-C-A

Variant summary

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

The ENST00000652818.1(ENSG00000287996):​n.415+40008C>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 0.177 in 151,888 control chromosomes in the GnomAD database, including 2,865 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 0.18 (2865 hom., cov: 31)
• Consequence: ENST00000652818.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903236	XR_007063922.1	n.415+40008C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652818.1	n.415+40008C>A		intron_variant, non_coding_transcript_variant
	ENST00000670475.1	n.928C>A		non_coding_transcript_exon_variant	2/2
	ENST00000656278.1	n.296-3879C>A		intron_variant, non_coding_transcript_variant
	ENST00000666997.1	n.513-21397C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26762 AN: 151770 Hom.: 2850 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.177 AC: 26816 AN: 151888 Hom.: 2865 Cov.: 31 AF XY: 0.182 AC XY: 13530 AN XY: 74194

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.184

Alfa AF: 0.157 Hom.: 232

Bravo AF: 0.184

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1905471; hg19: chr13-64011663;