chr3-99547493-C-T

Variant names:

• chr3-99547493-C-T
• rs13070584
• XR_001740466.3:n.475G>A

Variant summary

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

The XR_001740466.3(LOC105374005):​n.475G>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 0.0478 in 151,840 control chromosomes in the GnomAD database, including 284 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 0.048 (284 hom., cov: 32)
• Consequence: LOC105374005 XR_001740466.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 9 publications found

Genes affected

LOC105374005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374005	XR_001740466.3	n.475G>A		non_coding_transcript_exon_variant	Exon 1 of 6
LOC105374005	XR_007095985.1	n.475G>A		non_coding_transcript_exon_variant	Exon 1 of 5
LOC105374007	XR_001740463.2	n.96+42114G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243089	ENST00000742379.1	n.266+29665G>A		intron_variant	Intron 2 of 3
ENSG00000243089	ENST00000742380.1	n.266+29665G>A		intron_variant	Intron 2 of 6
ENSG00000243089	ENST00000742381.1	n.271+29665G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 7249 AN: 151722 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0256

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0478 AC: 7255 AN: 151840 Hom.: 284 Cov.: 32 AF XY: 0.0474 AC XY: 3519 AN XY: 74216

African (AFR) AF: 0.0472 AC: 1954 AN: 41420

American (AMR) AF: 0.0296 AC: 451 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1007 AN: 5138

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4816

European-Finnish (FIN) AF: 0.0131 AC: 138 AN: 10572

Middle Eastern (MID) AF: 0.0310 AC: 9 AN: 290

European-Non Finnish (NFE) AF: 0.0476 AC: 3231 AN: 67892

Other (OTH) AF: 0.0412 AC: 87 AN: 2110

Alfa AF: 0.0506 Hom.: 738

Bravo AF: 0.0486

Asia WGS AF: 0.0990 AC: 344 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.66
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs13070584; hg19: chr3-99266337;