rs4128340

Positions:

• chr4-87986984-C-A

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.307+2374G>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 0.343 in 151,924 control chromosomes in the GnomAD database, including 9,516 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 0.34 (9516 hom., cov: 32)
• Consequence: ENST00000662475.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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
	ENST00000662475.1	n.307+2374G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52128 AN: 151806 Hom.: 9511 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.343 AC: 52163 AN: 151924 Hom.: 9516 Cov.: 32 AF XY: 0.340 AC XY: 25276 AN XY: 74274

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.329

Alfa AF: 0.353 Hom.: 1181

Bravo AF: 0.334

Asia WGS AF: 0.131 AC: 454 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128340; hg19: chr4-88908136;