rs1588041

Positions:

• chr4-116225850-T-C

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.203-29113A>G 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 0.684 in 152,082 control chromosomes in the GnomAD database, including 41,913 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 0.68 (41913 hom., cov: 31)
• Consequence: ENST00000508414.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000508414.5	n.203-29113A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000509983.1	n.200-29113A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104086 AN: 151962 Hom.: 41914 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.684 AC: 104087 AN: 152082 Hom.: 41913 Cov.: 31 AF XY: 0.690 AC XY: 51300 AN XY: 74350

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.700

Alfa AF: 0.837 Hom.: 47487

Bravo AF: 0.654

Asia WGS AF: 0.777 AC: 2698 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1588041; hg19: chr4-117147006;