chr3-3617921-A-C

Variant names:

• chr3-3617921-A-C
• rs1386948
• ENST00000420000.6:n.200+8823T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):​n.200+8823T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,142 control chromosomes in the GnomAD database, including 43,197 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 0.75 (43197 hom., cov: 34)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.01

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 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+8823T>G		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114261 AN: 152024 Hom.: 43172 Cov.: 34

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.751 AC: 114333 AN: 152142 Hom.: 43197 Cov.: 34 AF XY: 0.749 AC XY: 55727 AN XY: 74386

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.755

Alfa AF: 0.787 Hom.: 69050

Bravo AF: 0.744

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1386948; hg19: chr3-3659605;