1-56385014-C-A

Position:

• chr1-56385014-C-A

Variant summary

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

The ENST00000641035.1(ENSG00000260971):​n.555+92119G>T 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 0.16 in 152,106 control chromosomes in the GnomAD database, including 2,617 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 0.16 (2617 hom., cov: 32)
• Consequence: ENST00000641035.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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
	ENST00000641035.1	n.555+92119G>T		intron_variant, non_coding_transcript_variant
	ENST00000641346.1	c.*269+15080G>T		intron_variant, NMD_transcript_variant				A2
	ENST00000641415.1	c.*95+98249G>T		intron_variant, NMD_transcript_variant				A2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24275 AN: 151988 Hom.: 2612 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.160 AC: 24316 AN: 152106 Hom.: 2617 Cov.: 32 AF XY: 0.157 AC XY: 11705 AN XY: 74364

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.0993

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.0934

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.132

Alfa AF: 0.107 Hom.: 2071

Bravo AF: 0.167

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11206801; hg19: chr1-56850686;