rs3754076

Positions:

• chr1-36083556-A-G
• chr1-36083556-A-T

Variant summary

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

The ENST00000446354.2(ENSG00000293245):​n.51+420T>C 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 0.759 in 152,016 control chromosomes in the GnomAD database, including 46,194 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 0.76 (46194 hom., cov: 32)
• Consequence: ENST00000446354.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 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
	ENST00000446354.2	n.51+420T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115363 AN: 151898 Hom.: 46190 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.759 AC: 115391 AN: 152016 Hom.: 46194 Cov.: 32 AF XY: 0.756 AC XY: 56155 AN XY: 74306

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.781

Alfa AF: 0.879 Hom.: 114421

Bravo AF: 0.731

Asia WGS AF: 0.704 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754076; hg19: chr1-36549157;