3-3617156-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000223727	ENST00000420000.6	n.200+9588T>C		intron_variant	Intron 2 of 4	4

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

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.507

Alfa AF: 0.501 Hom.: 34555

Bravo AF: 0.519

Asia WGS AF: 0.385 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1601875; hg19: chr3-3658840;