rs4122859

Positions:

• chr4-89675025-T-C

Variant summary

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

The ENST00000659878.1(ENSG00000251095):​n.480-51359T>C 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 0.153 in 152,138 control chromosomes in the GnomAD database, including 3,036 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 0.15 (3036 hom., cov: 31)
• Consequence: ENST00000659878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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
	ENST00000659878.1	n.480-51359T>C		intron_variant, non_coding_transcript_variant
	ENST00000673949.1	n.305+27249A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23260 AN: 152022 Hom.: 3024 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.0878

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.153 AC: 23299 AN: 152138 Hom.: 3036 Cov.: 31 AF XY: 0.152 AC XY: 11278 AN XY: 74396

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.0781

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0947 Hom.: 320

Bravo AF: 0.160

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4122859; hg19: chr4-90596176;