chr4-154142036-C-T

Position:

• chr4-154142036-C-T

Variant summary

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

The ENST00000660197.1(ENSG00000280241):​n.200-80C>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 0.903 in 152,168 control chromosomes in the GnomAD database, including 63,165 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 0.90 (63164 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENST00000660197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927947	XR_007058336.1	n.3959-80C>T		intron_variant, non_coding_transcript_variant
LOC101927947	XR_007058335.1	n.393-80C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660197.1	n.200-80C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137322 AN: 152048 Hom.: 63131 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.911

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.903 AC: 137401 AN: 152166 Hom.: 63164 Cov.: 31 AF XY: 0.905 AC XY: 67355 AN XY: 74390

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.993

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.912

Alfa AF: 0.938 Hom.: 8402

Bravo AF: 0.891

Asia WGS AF: 0.973 AC: 3378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.082
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4611909; hg19: chr4-155063188;