rs1905471

Variant names:

• chr13-63437530-C-A
• rs1905471
• ENST00000670475.1:n.928C>A

Variant summary

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

The ENST00000670475.1(ENSG00000287996):​n.928C>A variant causes a non coding transcript exon 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: ENSG00000287996 ENST00000670475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 1 publications found

Genes affected

ENSG00000287996 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903236	XR_007063922.1	n.415+40008C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287996	ENST00000670475.1	n.928C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287996	ENST00000652818.1	n.415+40008C>A		intron_variant	Intron 1 of 1
ENSG00000287996	ENST00000656278.1	n.296-3879C>A		intron_variant	Intron 1 of 2
ENSG00000287996	ENST00000666997.1	n.513-21397C>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.190 AC: 7877 AN: 41442

American (AMR) AF: 0.216 AC: 3295 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3472

East Asian (EAS) AF: 0.567 AC: 2895 AN: 5106

South Asian (SAS) AF: 0.226 AC: 1084 AN: 4806

European-Finnish (FIN) AF: 0.160 AC: 1695 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8959 AN: 67964

Other (OTH) AF: 0.184 AC: 388 AN: 2104

Alfa AF: 0.158 Hom.: 246

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1905471; hg19: chr13-64011663;