4-148634967-C-G

Position:

• chr4-148634967-C-G

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.222+90383C>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 0.468 in 151,846 control chromosomes in the GnomAD database, including 17,523 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 0.47 (17523 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986195	XR_001741441.2	n.3661+90383C>G		intron_variant, non_coding_transcript_variant
LOC105377483	XR_007058326.1	n.319-16166G>C		intron_variant, non_coding_transcript_variant
LOC105377483	XR_939336.4	n.319-16099G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661928.1	n.222+90383C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70924 AN: 151728 Hom.: 17494 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.468 AC: 71011 AN: 151846 Hom.: 17523 Cov.: 32 AF XY: 0.480 AC XY: 35624 AN XY: 74200

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.437

Alfa AF: 0.283 Hom.: 662

Bravo AF: 0.468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6845733; hg19: chr4-149556119;