rs4982270

Variant names:

• chr14-35411612-C-G
• rs4982270
• ENST00000848537.1:n.241+8225C>G

Your query was ambiguous. Multiple possible variants found:

• chr14-35411612-C-G
• chr14-35411612-C-T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+8225C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,016 control chromosomes in the GnomAD database, including 20,506 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 0.52 (20506 hom., cov: 32)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 8 publications found

Genes affected

ENSG00000310246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 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
ENSG00000310246	ENST00000848537.1	n.241+8225C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78969 AN: 151898 Hom.: 20484 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.520 AC: 79035 AN: 152016 Hom.: 20506 Cov.: 32 AF XY: 0.524 AC XY: 38953 AN XY: 74298

African (AFR) AF: 0.512 AC: 21212 AN: 41420

American (AMR) AF: 0.500 AC: 7640 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1741 AN: 3472

East Asian (EAS) AF: 0.682 AC: 3534 AN: 5180

South Asian (SAS) AF: 0.593 AC: 2855 AN: 4818

European-Finnish (FIN) AF: 0.571 AC: 6029 AN: 10550

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34518 AN: 67986

Other (OTH) AF: 0.515 AC: 1086 AN: 2110

Alfa AF: 0.506 Hom.: 2376

Bravo AF: 0.516

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.9
DANN	Benign	0.67
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs4982270; hg19: chr14-35880818;