3-3617156-A-G

Variant names:

• chr3-3617156-A-G
• rs1601875
• ENST00000420000.6:n.200+9588T>C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+9588T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,916 control chromosomes in the GnomAD database, including 21,183 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 0.52 (21183 hom., cov: 31)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 15 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420000.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.200+9588T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79294 AN: 151800 Hom.: 21164 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.522 AC: 79357 AN: 151916 Hom.: 21183 Cov.: 31 AF XY: 0.519 AC XY: 38545 AN XY: 74246

African (AFR) AF: 0.606 AC: 25066 AN: 41392

American (AMR) AF: 0.444 AC: 6783 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1426 AN: 5156

South Asian (SAS) AF: 0.401 AC: 1934 AN: 4820

European-Finnish (FIN) AF: 0.567 AC: 5974 AN: 10544

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34739 AN: 67952

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.509 Hom.: 53843

Bravo AF: 0.519

Asia WGS AF: 0.385 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.54
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1601875; hg19: chr3-3658840;