rs1287948

Variant names:

• chr1-226516024-G-C
• rs1287948
• ENST00000773545.1:n.208-31747G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000773545.1(ENSG00000300711):​n.208-31747G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 152,316 control chromosomes in the GnomAD database, including 67,322 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 0.94 (67322 hom., cov: 33)
• Consequence: ENSG00000300711 ENST00000773545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 2 publications found

Genes affected

ENSG00000300711 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373115	XR_949220.2	n.*120C>G		downstream_gene_variant
LOC105373115	XR_949221.2	n.*120C>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300711	ENST00000773545.1	n.208-31747G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.940 AC: 143063 AN: 152198 Hom.: 67267 Cov.: 33

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.940 AC: 143180 AN: 152316 Hom.: 67322 Cov.: 33 AF XY: 0.941 AC XY: 70073 AN XY: 74474

African (AFR) AF: 0.940 AC: 39091 AN: 41568

American (AMR) AF: 0.955 AC: 14616 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3034 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4983 AN: 5186

South Asian (SAS) AF: 0.948 AC: 4566 AN: 4814

European-Finnish (FIN) AF: 0.946 AC: 10046 AN: 10622

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63764 AN: 68034

Other (OTH) AF: 0.938 AC: 1980 AN: 2110

Alfa AF: 0.944 Hom.: 8513

Bravo AF: 0.940

Asia WGS AF: 0.947 AC: 3294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1287948; hg19: chr1-226703725;