4-116189949-A-T

Variant names:

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

Variant summary

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

The ENST00000508414.5(ENSG00000249259):​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: ENSG00000249259 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

ENSG00000249259 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000249259	ENST00000508414.5	n.336+6655T>A		intron_variant	Intron 2 of 2	3
ENSG00000249259	ENST00000509983.1	n.333+6655T>A		intron_variant	Intron 2 of 2	3

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.704

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395433; hg19: chr4-117111105;