4-87975269-T-C

Position:

• chr4-87975269-T-C

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.901A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,224 control chromosomes in the GnomAD database, including 12,625 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 0.37 (12625 hom., cov: 33)
• Consequence: ENST00000662475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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.901A>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56993 AN: 152106 Hom.: 12625 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.374 AC: 56998 AN: 152224 Hom.: 12625 Cov.: 33 AF XY: 0.375 AC XY: 27888 AN XY: 74430

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.409

Alfa AF: 0.464 Hom.: 17545

Bravo AF: 0.365

Asia WGS AF: 0.414 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
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: rs11730582; hg19: chr4-88896421;