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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268225	XR_007066048.1	n.8945T>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC112268225	XR_007066049.1	n.7647-551T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MED8-AS1	ENST00000752857.1	n.317T>A		non_coding_transcript_exon_variant	Exon 2 of 2
MED8-AS1	ENST00000752766.1	n.214-7810T>A		intron_variant	Intron 2 of 2
MED8-AS1	ENST00000752767.1	n.389-7810T>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs4141740; hg19: chr1-43842827; COSMIC: COSV59170778;