7-143224141-C-T

Variant names:

• chr7-143224141-C-T
• rs534126
• ENST00000624211.1:n.94G>A

Variant summary

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

The ENST00000624211.1(ENSG00000279223):​n.94G>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 0.384 in 152,042 control chromosomes in the GnomAD database, including 13,371 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 0.38 (13371 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENSG00000279223 ENST00000624211.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 9 publications found

Genes affected

ENSG00000279223 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279223	ENST00000624211.1	n.94G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58252 AN: 151912 Hom.: 13334 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.395

GnomAD4 exome AF: 0.167 AC: 2 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 2 AN XY: 12

African (AFR) AF: 0.500 AC: 1 AN: 2

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: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.384 AC: 58335 AN: 152030 Hom.: 13371 Cov.: 32 AF XY: 0.373 AC XY: 27740 AN XY: 74338

African (AFR) AF: 0.634 AC: 26274 AN: 41424

American (AMR) AF: 0.293 AC: 4476 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3472

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5182

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2065 AN: 10578

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21164 AN: 67986

Other (OTH) AF: 0.394 AC: 831 AN: 2108

Alfa AF: 0.334 Hom.: 23783

Bravo AF: 0.403

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.51
DANN	Benign	0.40
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs534126; hg19: chr7-142921234;