rs4810624

Variant names:

• chr20-37414503-T-C
• rs4810624
• ENST00000811047.1:n.167+1946T>C

Variant summary

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

The ENST00000811047.1(ENSG00000305458):​n.167+1946T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 150,556 control chromosomes in the GnomAD database, including 278 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 0.045 (278 hom., cov: 27)
• Consequence: ENSG00000305458 ENST00000811047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

Genes affected

ENSG00000305458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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
ENSG00000305458	ENST00000811047.1	n.167+1946T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0453 AC: 6819 AN: 150434 Hom.: 280 Cov.: 27

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0355

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0454 AC: 6830 AN: 150556 Hom.: 278 Cov.: 27 AF XY: 0.0465 AC XY: 3415 AN XY: 73492

African (AFR) AF: 0.0275 AC: 1124 AN: 40876

American (AMR) AF: 0.104 AC: 1577 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.0511 AC: 177 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1072 AN: 4968

South Asian (SAS) AF: 0.0353 AC: 167 AN: 4730

European-Finnish (FIN) AF: 0.0182 AC: 190 AN: 10458

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0346 AC: 2343 AN: 67670

Other (OTH) AF: 0.0553 AC: 115 AN: 2080

Alfa AF: 0.0424 Hom.: 404

Bravo AF: 0.0536

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.55
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4810624; hg19: chr20-36042906;