rs1103021

Positions:

• chr4-116067741-G-A
• chr4-116067741-G-T

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.336+128863C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,894 control chromosomes in the GnomAD database, including 38,214 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 0.70 (38214 hom., cov: 31)
• Consequence: ENST00000508414.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000508414.5	n.336+128863C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106234 AN: 151776 Hom.: 38152 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.700 AC: 106354 AN: 151894 Hom.: 38214 Cov.: 31 AF XY: 0.701 AC XY: 52030 AN XY: 74232

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.681

Alfa AF: 0.653 Hom.: 3915

Bravo AF: 0.713

Asia WGS AF: 0.684 AC: 2377 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1103021; hg19: chr4-116988897;