rs583341

Variant names:

• chr6-144279834-A-G
• rs583341
• ENST00000788251.1:n.115+4900T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-144279834-A-G
• chr6-144279834-A-T

Variant summary

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

The ENST00000788251.1(ENSG00000302628):​n.115+4900T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,128 control chromosomes in the GnomAD database, including 19,024 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 0.49 (19024 hom., cov: 33)
• Consequence: ENSG00000302628 ENST00000788251.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 3 publications found

Genes affected

ENSG00000302628 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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
ENSG00000302628	ENST00000788251.1	n.115+4900T>C		intron_variant	Intron 1 of 3
ENSG00000302628	ENST00000788252.1	n.150+4900T>C		intron_variant	Intron 1 of 2
ENSG00000302628	ENST00000788253.1	n.100+4900T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74688 AN: 152010 Hom.: 18992 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.492 AC: 74779 AN: 152128 Hom.: 19024 Cov.: 33 AF XY: 0.488 AC XY: 36288 AN XY: 74362

African (AFR) AF: 0.616 AC: 25559 AN: 41522

American (AMR) AF: 0.474 AC: 7244 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2874 AN: 5178

South Asian (SAS) AF: 0.543 AC: 2617 AN: 4822

European-Finnish (FIN) AF: 0.369 AC: 3905 AN: 10578

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29142 AN: 67956

Other (OTH) AF: 0.495 AC: 1047 AN: 2116

Alfa AF: 0.460 Hom.: 6284

Bravo AF: 0.504

Asia WGS AF: 0.553 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.75
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs583341; hg19: chr6-144600970;