rs4141741

Variant names:

• chr1-43377329-C-T
• rs4141741
• ENST00000752857.1:n.490C>T

Variant summary

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

The ENST00000752857.1(MED8-AS1):​n.490C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,034 control chromosomes in the GnomAD database, including 8,238 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 0.32 (8238 hom., cov: 32)
• Consequence: MED8-AS1 ENST00000752857.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 12 publications found

Genes affected

MED8-AS1 (HGNC:40908): (MED8 antisense RNA 1)

LOC112268225 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MED8-AS1	ENST00000752857.1		n.490C>T		non_coding_transcript_exon	Exon 2 of 2
	MED8-AS1	ENST00000752766.1		n.214-7637C>T		intron	N/A
	MED8-AS1	ENST00000752767.1		n.389-7637C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48986 AN: 151916 Hom.: 8235 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.322 AC: 49019 AN: 152034 Hom.: 8238 Cov.: 32 AF XY: 0.318 AC XY: 23626 AN XY: 74304

African (AFR) AF: 0.260 AC: 10784 AN: 41438

American (AMR) AF: 0.368 AC: 5615 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3472

East Asian (EAS) AF: 0.0988 AC: 512 AN: 5182

South Asian (SAS) AF: 0.148 AC: 714 AN: 4824

European-Finnish (FIN) AF: 0.331 AC: 3493 AN: 10568

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25233 AN: 67972

Other (OTH) AF: 0.374 AC: 789 AN: 2110

Alfa AF: 0.346 Hom.: 1933

Bravo AF: 0.325

Asia WGS AF: 0.144 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.67
PhyloP100		-0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4141741;

hg19: chr1-43843000;