chr5-127688390-T-C

Variant names:

• chr5-127688390-T-C
• rs3910198
• ENST00000827053.1:n.194+14337A>G

Variant summary

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

The ENST00000827053.1(ENSG00000248799):​n.194+14337A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151,866 control chromosomes in the GnomAD database, including 29,685 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 0.62 (29685 hom., cov: 31)
• Consequence: ENSG00000248799 ENST00000827053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 2 publications found

Genes affected

ENSG00000248799 (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 (NFE) allele frequency at 95% confidence interval = 0.652 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
ENSG00000248799	ENST00000827053.1	n.194+14337A>G		intron_variant	Intron 1 of 3
ENSG00000248799	ENST00000827054.1	n.199-5102A>G		intron_variant	Intron 2 of 2
ENSG00000248799	ENST00000827055.1	n.253-5102A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93967 AN: 151750 Hom.: 29643 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.619 AC: 94049 AN: 151866 Hom.: 29685 Cov.: 31 AF XY: 0.613 AC XY: 45490 AN XY: 74216

African (AFR) AF: 0.640 AC: 26504 AN: 41428

American (AMR) AF: 0.492 AC: 7499 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3468

East Asian (EAS) AF: 0.354 AC: 1826 AN: 5152

South Asian (SAS) AF: 0.486 AC: 2338 AN: 4812

European-Finnish (FIN) AF: 0.670 AC: 7072 AN: 10552

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44644 AN: 67916

Other (OTH) AF: 0.595 AC: 1255 AN: 2108

Alfa AF: 0.620 Hom.: 11496

Bravo AF: 0.604

Asia WGS AF: 0.405 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs3910198; hg19: chr5-127024082;