chr4-99469947-A-C

Position:

• chr4-99469947-A-C

Variant summary

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

The ENST00000506494.1(ENSG00000250300):​n.440-131T>G 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 0.365 in 152,054 control chromosomes in the GnomAD database, including 11,092 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 0.36 (11091 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: ENST00000506494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000506494.1	n.440-131T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55428 AN: 151928 Hom.: 11086 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.365 AC: 55472 AN: 152048 Hom.: 11091 Cov.: 32 AF XY: 0.366 AC XY: 27182 AN XY: 74340

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.346

Alfa AF: 0.423 Hom.: 18655

Bravo AF: 0.356

Asia WGS AF: 0.340 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851024; hg19: chr4-100391104;