rs853184

Variant names:

• chr5-143261336-C-T
• rs853184
• ENST00000770709.1:n.117+2043C>T

Variant summary

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

The ENST00000770709.1(ENSG00000300303):​n.117+2043C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,232 control chromosomes in the GnomAD database, including 1,548 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 0.13 (1548 hom., cov: 31)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 5 publications found

Genes affected

ENSG00000300303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300303	ENST00000770709.1	n.117+2043C>T		intron_variant	Intron 1 of 3
ENSG00000300303	ENST00000770710.1	n.117+2043C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20478 AN: 152114 Hom.: 1544 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.135 AC: 20515 AN: 152232 Hom.: 1548 Cov.: 31 AF XY: 0.134 AC XY: 9961 AN XY: 74426

African (AFR) AF: 0.127 AC: 5272 AN: 41532

American (AMR) AF: 0.0775 AC: 1186 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3468

East Asian (EAS) AF: 0.0711 AC: 369 AN: 5190

South Asian (SAS) AF: 0.0321 AC: 155 AN: 4828

European-Finnish (FIN) AF: 0.211 AC: 2234 AN: 10582

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10623 AN: 68014

Other (OTH) AF: 0.111 AC: 235 AN: 2114

Alfa AF: 0.138 Hom.: 2519

Bravo AF: 0.125

Asia WGS AF: 0.0690 AC: 241 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.73
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs853184; hg19: chr5-142640901;