3-3616902-C-T

Variant names:

• chr3-3616902-C-T
• rs1601876
• ENST00000420000.6:n.200+9842G>A

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+9842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,112 control chromosomes in the GnomAD database, including 38,271 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 0.71 (38271 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.200+9842G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107296 AN: 151992 Hom.: 38246 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.706 AC: 107375 AN: 152112 Hom.: 38271 Cov.: 32 AF XY: 0.705 AC XY: 52446 AN XY: 74368

African (AFR) AF: 0.615 AC: 25526 AN: 41478

American (AMR) AF: 0.686 AC: 10484 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2321 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3389 AN: 5156

South Asian (SAS) AF: 0.704 AC: 3390 AN: 4818

European-Finnish (FIN) AF: 0.793 AC: 8404 AN: 10600

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51431 AN: 67992

Other (OTH) AF: 0.715 AC: 1511 AN: 2112

Alfa AF: 0.721 Hom.: 22306

Bravo AF: 0.692

Asia WGS AF: 0.660 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.36
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1601876; hg19: chr3-3658586;