rs4141740

Variant names:

• chr1-43377156-T-A
• rs4141740
• ENST00000752857.1:n.317T>A

Variant summary

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

The ENST00000752857.1(MED8-AS1):​n.317T>A 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 0.316 in 151,990 control chromosomes in the GnomAD database, including 8,004 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 (8004 hom., cov: 32)
• Consequence: MED8-AS1 ENST00000752857.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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.317T>A		non_coding_transcript_exon	Exon 2 of 2
	MED8-AS1	ENST00000752766.1		n.214-7810T>A		intron	N/A
	MED8-AS1	ENST00000752767.1		n.389-7810T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48029 AN: 151872 Hom.: 8002 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.316 AC: 48061 AN: 151990 Hom.: 8004 Cov.: 32 AF XY: 0.312 AC XY: 23162 AN XY: 74298

African (AFR) AF: 0.238 AC: 9847 AN: 41434

American (AMR) AF: 0.366 AC: 5596 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3472

East Asian (EAS) AF: 0.0986 AC: 511 AN: 5182

South Asian (SAS) AF: 0.148 AC: 710 AN: 4802

European-Finnish (FIN) AF: 0.332 AC: 3506 AN: 10558

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

European-Non Finnish (NFE) AF: 0.371 AC: 25237 AN: 67952

Other (OTH) AF: 0.368 AC: 773 AN: 2102

Alfa AF: 0.340 Hom.: 1125

Bravo AF: 0.318

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.44
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: rs4141740;

hg19: chr1-43842827;

COSMIC: COSV59170778;