rs2816316

Positions:

• chr1-192567683-C-A
• chr1-192567683-C-G

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.526-467G>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 0.788 in 152,094 control chromosomes in the GnomAD database, including 47,510 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 0.79 (47510 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.288-467G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644134.1	n.526-467G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119810 AN: 151976 Hom.: 47485 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.788 AC: 119877 AN: 152094 Hom.: 47510 Cov.: 32 AF XY: 0.794 AC XY: 58991 AN XY: 74338

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.788

Alfa AF: 0.816 Hom.: 106491

Bravo AF: 0.778

Asia WGS AF: 0.854 AC: 2969 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2816316; hg19: chr1-192536813;