rs3098212

Variant names:

• chr8-103452121-T-C
• rs3098212
• ENST00000649416.1:c.1+37576A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000649416.1(ENSG00000285982):​c.1+37576A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,184 control chromosomes in the GnomAD database, including 4,266 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 0.23 (4266 hom., cov: 32)
• Consequence: ENSG00000285982 ENST00000649416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 3 publications found

Genes affected

ENSG00000285982 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 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
ENSG00000285982	ENST00000649416.1	c.1+37576A>G		intron_variant	Intron 3 of 8			ENSP00000496817.1
ENSG00000288945	ENST00000690469.1	n.991T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35447 AN: 152066 Hom.: 4256 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.233 AC: 35486 AN: 152184 Hom.: 4266 Cov.: 32 AF XY: 0.238 AC XY: 17696 AN XY: 74412

African (AFR) AF: 0.213 AC: 8861 AN: 41520

American (AMR) AF: 0.239 AC: 3659 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1774 AN: 5170

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2975 AN: 10598

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15522 AN: 68006

Other (OTH) AF: 0.234 AC: 495 AN: 2112

Alfa AF: 0.230 Hom.: 2100

Bravo AF: 0.229

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	6.4
DANN	Benign	0.77
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs3098212; hg19: chr8-104464349;