rs4467881

Positions:

• chr7-129770304-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710872.1(ENSG00000286380):​n.432-6898C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 437,738 control chromosomes in the GnomAD database, including 64,838 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 0.56 (24652 hom., cov: 32)
  • Exomes 𝑓: 0.51 (40186 hom.)
• Consequence: ENST00000710872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000710872.1	n.432-6898C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84923 AN: 151900 Hom.: 24633 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.551

GnomAD4 exome AF: 0.515 AC: 147086 AN: 285720 Hom.: 40186 AF XY: 0.507 AC XY: 80534 AN XY: 158968

Gnomad4 AFR exome AF: 0.586

Gnomad4 AMR exome AF: 0.427

Gnomad4 ASJ exome AF: 0.653

Gnomad4 EAS exome AF: 0.0456

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.504

Gnomad4 NFE exome AF: 0.593

Gnomad4 OTH exome AF: 0.549

GnomAD4 genome AF: 0.559 AC: 84983 AN: 152018 Hom.: 24652 Cov.: 32 AF XY: 0.550 AC XY: 40889 AN XY: 74324

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.545

Alfa AF: 0.589 Hom.: 5352

Bravo AF: 0.557

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4467881; hg19: chr7-129410144; COSMIC: COSV63012826;