chr1-196851157-A-G

Position:

• chr1-196851157-A-G

Variant summary

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

The ENST00000649395.1(ENSG00000285986):​n.58+817A>G 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 0.659 in 150,806 control chromosomes in the GnomAD database, including 33,577 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 0.66 (33577 hom., cov: 32)
• Consequence: ENST00000649395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649395.1	n.58+817A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99324 AN: 150690 Hom.: 33548 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.708

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.659 AC: 99391 AN: 150806 Hom.: 33577 Cov.: 32 AF XY: 0.658 AC XY: 48468 AN XY: 73652

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.644

Alfa AF: 0.662 Hom.: 4190

Bravo AF: 0.652

Asia WGS AF: 0.598 AC: 2077 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs503002; hg19: chr1-196820287;