4-62194862-T-C

Variant names:

• chr4-62194862-T-C
• rs4446347
• ENST00000676649.1:n.447-25469T>C

Variant summary

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

The ENST00000676649.1(ENSG00000288659):​n.447-25469T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,716 control chromosomes in the GnomAD database, including 28,201 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 0.61 (28201 hom., cov: 30)
• Consequence: ENSG00000288659 ENST00000676649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 2 publications found

Genes affected

ENSG00000288659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676649.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288659	ENST00000676649.1		n.447-25469T>C		intron	N/A
	ENSG00000288659	ENST00000687436.3		n.416-25469T>C		intron	N/A
	ENSG00000288659	ENST00000702460.2		n.287-19787T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91718 AN: 151596 Hom.: 28158 Cov.: 30

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.605 AC: 91821 AN: 151716 Hom.: 28201 Cov.: 30 AF XY: 0.603 AC XY: 44662 AN XY: 74126

African (AFR) AF: 0.697 AC: 28829 AN: 41374

American (AMR) AF: 0.620 AC: 9441 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2012 AN: 3472

East Asian (EAS) AF: 0.585 AC: 2986 AN: 5104

South Asian (SAS) AF: 0.485 AC: 2327 AN: 4798

European-Finnish (FIN) AF: 0.565 AC: 5937 AN: 10512

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.563 AC: 38269 AN: 67918

Other (OTH) AF: 0.619 AC: 1303 AN: 2106

Alfa AF: 0.581 Hom.: 32790

Bravo AF: 0.615

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4446347; hg19: chr4-63060580;