chr14-101073047-C-T

Variant names:

• chr14-101073047-C-T
• rs7147503
• ENST00000818881.1:n.1426G>A

Variant summary

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

The ENST00000818881.1(ENSG00000230805):​n.1426G>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 0.327 in 152,260 control chromosomes in the GnomAD database, including 9,043 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 0.33 (9042 hom., cov: 34)
  • Exomes 𝑓: 0.30 (1 hom.)
• Consequence: ENSG00000230805 ENST00000818881.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 20 publications found

Genes affected

ENSG00000230805 (HGNC:):

MEG9 (HGNC:43874): (maternally expressed 9)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818881.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105370670	NR_188195.1		n.1084-147G>A		intron	N/A
	MEG9	NR_047664.1		n.*110C>T		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230805	ENST00000818881.1		n.1426G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000230805	ENST00000448840.8	TSL:3	n.1107-147G>A		intron	N/A
	ENSG00000230805	ENST00000673125.1		n.571-147G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49832 AN: 152112 Hom.: 9040 Cov.: 34

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.329

GnomAD4 exome AF: 0.300 AC: 9 AN: 30 Hom.: 1 AF XY: 0.0833 AC XY: 1 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.429 AC: 6 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.327 AC: 49845 AN: 152230 Hom.: 9042 Cov.: 34 AF XY: 0.335 AC XY: 24939 AN XY: 74404

African (AFR) AF: 0.169 AC: 7018 AN: 41550

American (AMR) AF: 0.359 AC: 5486 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1116 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2378 AN: 5162

South Asian (SAS) AF: 0.410 AC: 1981 AN: 4828

European-Finnish (FIN) AF: 0.509 AC: 5395 AN: 10600

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25377 AN: 67996

Other (OTH) AF: 0.328 AC: 693 AN: 2116

Alfa AF: 0.351 Hom.: 28683

Bravo AF: 0.312

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.88
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs7147503; hg19: chr14-101539384;