rs6056923

Variant names:

• chr20-9840271-T-C
• rs6056923
• ENST00000656748.1:n.176+4230T>C

Variant summary

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

The ENST00000656748.1(ENSG00000286470):​n.176+4230T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 152,238 control chromosomes in the GnomAD database, including 1,971 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 0.10 (1971 hom., cov: 32)
• Consequence: ENSG00000286470 ENST00000656748.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 1 publications found

Genes affected

ENSG00000286470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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
ENSG00000286470	ENST00000656748.1	n.176+4230T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0993 AC: 15101 AN: 152120 Hom.: 1949 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0788

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

GnomAD4 genome AF: 0.0997 AC: 15178 AN: 152238 Hom.: 1971 Cov.: 32 AF XY: 0.0967 AC XY: 7196 AN XY: 74442

African (AFR) AF: 0.303 AC: 12553 AN: 41488

American (AMR) AF: 0.0417 AC: 638 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5184

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4832

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10620

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0177 AC: 1202 AN: 68020

Other (OTH) AF: 0.0789 AC: 167 AN: 2116

Alfa AF: 0.0648 Hom.: 143

Bravo AF: 0.111

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs6056923; hg19: chr20-9820919;