rs17600303

Variant names:

• chr4-44515687-C-G
• rs17600303
• ENST00000758081.1:n.310+8913C>G

Variant summary

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

The ENST00000758081.1(ENSG00000298812):​n.310+8913C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0356 in 151,778 control chromosomes in the GnomAD database, including 227 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 0.036 (227 hom., cov: 30)
• Consequence: ENSG00000298812 ENST00000758081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 0 publications found

Genes affected

ENSG00000298812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0853 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
ENSG00000298812	ENST00000758081.1	n.310+8913C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5388 AN: 151660 Hom.: 229 Cov.: 30

Gnomad AFR AF: 0.0878

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.00722

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00653

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0356 AC: 5397 AN: 151778 Hom.: 227 Cov.: 30 AF XY: 0.0372 AC XY: 2761 AN XY: 74142

African (AFR) AF: 0.0876 AC: 3622 AN: 41330

American (AMR) AF: 0.0202 AC: 307 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3470

East Asian (EAS) AF: 0.0874 AC: 449 AN: 5138

South Asian (SAS) AF: 0.0869 AC: 418 AN: 4808

European-Finnish (FIN) AF: 0.00722 AC: 76 AN: 10528

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00653 AC: 444 AN: 67970

Other (OTH) AF: 0.0299 AC: 63 AN: 2110

Alfa AF: 0.0225 Hom.: 16

Bravo AF: 0.0380

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0070
DANN	Benign	0.42
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs17600303; hg19: chr4-44517704;