rs6104740

Variant names:

• chr20-11356161-C-A
• rs6104740
• ENST00000784589.1:n.76-414G>T

Variant summary

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

The ENST00000784589.1(ENSG00000302131):​n.76-414G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,934 control chromosomes in the GnomAD database, including 8,424 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 0.32 (8424 hom., cov: 32)
• Consequence: ENSG00000302131 ENST00000784589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 2 publications found

Genes affected

ENSG00000302131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372529	XR_937261.2	n.58-414G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302131	ENST00000784589.1	n.76-414G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48323 AN: 151816 Hom.: 8399 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.319 AC: 48393 AN: 151934 Hom.: 8424 Cov.: 32 AF XY: 0.314 AC XY: 23349 AN XY: 74266

African (AFR) AF: 0.453 AC: 18765 AN: 41416

American (AMR) AF: 0.279 AC: 4261 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3466

East Asian (EAS) AF: 0.447 AC: 2309 AN: 5168

South Asian (SAS) AF: 0.358 AC: 1723 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1916 AN: 10538

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17486 AN: 67948

Other (OTH) AF: 0.300 AC: 632 AN: 2106

Alfa AF: 0.172 Hom.: 371

Bravo AF: 0.334

Asia WGS AF: 0.418 AC: 1450 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.19
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6104740; hg19: chr20-11336809;