chr4-43775353-G-A

Position:

• chr4-43775353-G-A

Variant summary

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

The ENST00000655512.1(ENSG00000286891):​n.117-3175G>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 0.274 in 150,008 control chromosomes in the GnomAD database, including 5,764 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 0.27 (5764 hom., cov: 28)
• Consequence: ENST00000655512.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655512.1	n.117-3175G>A		intron_variant, non_coding_transcript_variant
	ENST00000665455.1	n.286+11578G>A		intron_variant, non_coding_transcript_variant
	ENST00000667550.1	n.310-3175G>A		intron_variant, non_coding_transcript_variant
	ENST00000669927.1	n.282-3175G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41079 AN: 149892 Hom.: 5757 Cov.: 28

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.274 AC: 41096 AN: 150008 Hom.: 5764 Cov.: 28 AF XY: 0.269 AC XY: 19685 AN XY: 73094

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.246

Alfa AF: 0.265 Hom.: 6683

Bravo AF: 0.281

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.71
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1713511; hg19: chr4-43777370;