rs947211

Positions:

• chr1-205783537-A-G

Variant summary

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

The ENST00000648961.1(ENSG00000285521):​n.1069A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,122 control chromosomes in the GnomAD database, including 32,891 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 0.64 (32891 hom., cov: 33)
• Consequence: ENST00000648961.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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
	ENST00000648961.1	n.1069A>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97249 AN: 152004 Hom.: 32876 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.640 AC: 97294 AN: 152122 Hom.: 32891 Cov.: 33 AF XY: 0.637 AC XY: 47413 AN XY: 74404

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.669

Alfa AF: 0.730 Hom.: 67689

Bravo AF: 0.611

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947211; hg19: chr1-205752665;