rs997973

Variant names:

• chr1-191148468-A-G
• rs997973
• ENST00000648197.1:n.201+2742T>C

Variant summary

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

The ENST00000648197.1(ENSG00000285638):​n.201+2742T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 152,196 control chromosomes in the GnomAD database, including 752 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 0.060 (752 hom., cov: 32)
• Consequence: ENSG00000285638 ENST00000648197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 1 publications found

Genes affected

ENSG00000285638 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 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
ENSG00000285638	ENST00000648197.1	n.201+2742T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9142 AN: 152078 Hom.: 749 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0245

Gnomad ASJ AF: 0.000866

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00925

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0603 AC: 9174 AN: 152196 Hom.: 752 Cov.: 32 AF XY: 0.0595 AC XY: 4430 AN XY: 74434

African (AFR) AF: 0.185 AC: 7668 AN: 41486

American (AMR) AF: 0.0245 AC: 375 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000866 AC: 3 AN: 3466

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5178

South Asian (SAS) AF: 0.0503 AC: 243 AN: 4828

European-Finnish (FIN) AF: 0.00122 AC: 13 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00925 AC: 629 AN: 68004

Other (OTH) AF: 0.0483 AC: 102 AN: 2110

Alfa AF: 0.0297 Hom.: 103

Bravo AF: 0.0677

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs997973; hg19: chr1-191117598;