4-177298634-C-T

Position:

• chr4-177298634-C-T

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.112+2413G>A 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 0.228 in 150,950 control chromosomes in the GnomAD database, including 5,132 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 0.23 (5132 hom., cov: 32)
• Consequence: ENST00000656694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377557	XR_001741925.2	n.234+2413G>A		intron_variant, non_coding_transcript_variant
LOC105377557	XR_007058380.1	n.234+2413G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656694.1	n.112+2413G>A		intron_variant, non_coding_transcript_variant
	ENST00000662794.1	n.61+2413G>A		intron_variant, non_coding_transcript_variant
	ENST00000667713.1	n.207+2413G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34389 AN: 150832 Hom.: 5098 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.228 AC: 34472 AN: 150950 Hom.: 5132 Cov.: 32 AF XY: 0.232 AC XY: 17061 AN XY: 73672

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.204

Alfa AF: 0.163 Hom.: 1461

Bravo AF: 0.236

Asia WGS AF: 0.244 AC: 838 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1983132; hg19: chr4-178219788;