4-116189949-A-T

Variant names:

• chr4-116189949-A-T
• rs1395433
• ENST00000508414.5:n.336+6655T>A

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.336+6655T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,022 control chromosomes in the GnomAD database, including 42,623 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 0.69 (42623 hom., cov: 32)
• Consequence: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 1 publications found

Genes affected

ENSG00000293005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508414.5. 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
	ENSG00000293005	ENST00000508414.5	TSL:3	n.336+6655T>A		intron	N/A
	ENSG00000293005	ENST00000509983.2	TSL:3	n.398+6655T>A		intron	N/A
	ENSG00000293005	ENST00000775331.1		n.545+6655T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105437 AN: 151904 Hom.: 42624 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.694 AC: 105437 AN: 152022 Hom.: 42623 Cov.: 32 AF XY: 0.701 AC XY: 52102 AN XY: 74302

African (AFR) AF: 0.243 AC: 10054 AN: 41438

American (AMR) AF: 0.781 AC: 11906 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2842 AN: 3468

East Asian (EAS) AF: 0.899 AC: 4652 AN: 5174

South Asian (SAS) AF: 0.861 AC: 4152 AN: 4820

European-Finnish (FIN) AF: 0.932 AC: 9870 AN: 10592

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59373 AN: 67962

Other (OTH) AF: 0.704 AC: 1486 AN: 2110

Alfa AF: 0.701 Hom.: 2694

Bravo AF: 0.660

Asia WGS AF: 0.819 AC: 2832 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.27
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1395433; hg19: chr4-117111105;