chr4-176681014-A-T

Position:

• chr4-176681014-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000504017.5(ENSG00000248388):​n.140+1264A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,104 control chromosomes in the GnomAD database, including 28,223 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 0.58 (28223 hom., cov: 32)
• Consequence: ENSG00000248388 ENST00000504017.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

ENSG00000248388 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HAFML	NR_183975.1	n.182+11305A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248388	ENST00000504017.5	n.140+1264A>T		intron_variant		2
ENSG00000248388	ENST00000509194.1	n.89+11305A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88730 AN: 151986 Hom.: 28233 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.583 AC: 88744 AN: 152104 Hom.: 28223 Cov.: 32 AF XY: 0.593 AC XY: 44094 AN XY: 74376

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.597

Alfa AF: 0.495 Hom.: 1530

Bravo AF: 0.557

Asia WGS AF: 0.699 AC: 2426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	13
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1385736; hg19: chr4-177602165;