rs3218121

Variant names:

• chr1-23531825-G-A
• rs3218121
• ENST00000826972.1:n.203+4755G>A

Variant summary

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

The ENST00000826972.1(ENSG00000307540):​n.203+4755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 152,236 control chromosomes in the GnomAD database, including 352 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 0.064 (352 hom., cov: 32)
• Consequence: ENSG00000307540 ENST00000826972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 11 publications found

Genes affected

ENSG00000307540 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 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
ENSG00000307540	ENST00000826972.1	n.203+4755G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9744 AN: 152118 Hom.: 351 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0581

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0641 AC: 9756 AN: 152236 Hom.: 352 Cov.: 32 AF XY: 0.0629 AC XY: 4683 AN XY: 74446

African (AFR) AF: 0.0495 AC: 2055 AN: 41548

American (AMR) AF: 0.0450 AC: 689 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.120 AC: 578 AN: 4820

European-Finnish (FIN) AF: 0.0581 AC: 617 AN: 10612

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0760 AC: 5166 AN: 68004

Other (OTH) AF: 0.0655 AC: 138 AN: 2108

Alfa AF: 0.0763 Hom.: 784

Bravo AF: 0.0621

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.5
DANN	Benign	0.84
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs3218121; hg19: chr1-23858317;