rs3767488

Positions:

• chr1-192812509-A-G

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.105-46315T>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 0.485 in 72,724 control chromosomes in the GnomAD database, including 4,567 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 0.49 (4567 hom., cov: 29)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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
	ENST00000644134.1	n.105-46315T>C		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-46315T>C		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.199+14395T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 35296 AN: 72722 Hom.: 4565 Cov.: 29

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.489

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.485 AC: 35296 AN: 72724 Hom.: 4567 Cov.: 29 AF XY: 0.485 AC XY: 17401 AN XY: 35870

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.485

Alfa AF: 0.233 Hom.: 466

Bravo AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3767488; hg19: chr1-192781639;