rs947211

Variant names:

• chr1-205783537-A-G
• rs947211
• ENST00000648961.1:n.1069A>G

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000285521 ENST00000648961.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02
• Publications: 76 publications found

Genes affected

ENSG00000285521 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285521	ENST00000648961.1	n.1069A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285521	ENST00000839048.1	n.1009A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000285521	ENST00000839049.1	n.1187A>G		non_coding_transcript_exon_variant	Exon 2 of 2

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

African (AFR) AF: 0.437 AC: 18142 AN: 41474

American (AMR) AF: 0.566 AC: 8646 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2592 AN: 3472

East Asian (EAS) AF: 0.536 AC: 2776 AN: 5176

South Asian (SAS) AF: 0.600 AC: 2892 AN: 4816

European-Finnish (FIN) AF: 0.785 AC: 8313 AN: 10584

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51645 AN: 68006

Other (OTH) AF: 0.669 AC: 1411 AN: 2110

Alfa AF: 0.717 Hom.: 156220

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
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs947211; hg19: chr1-205752665;