rs1514135

Variant names:

• chr1-55650559-C-G
• rs1514135
• ENST00000422374.1:n.240+35557C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-55650559-C-G
• chr1-55650559-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422374.1(ENSG00000234810):​n.240+35557C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,012 control chromosomes in the GnomAD database, including 16,512 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 0.44 (16512 hom., cov: 32)
• Consequence: ENSG00000234810 ENST00000422374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

ENSG00000234810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 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
ENSG00000234810	ENST00000422374.1	n.240+35557C>G		intron_variant	Intron 2 of 2	2
ENSG00000234810	ENST00000634769.1	n.217-22701C>G		intron_variant	Intron 2 of 3	5
ENSG00000234810	ENST00000643167.1	n.221-22701C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67476 AN: 151894 Hom.: 16480 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.444 AC: 67568 AN: 152012 Hom.: 16512 Cov.: 32 AF XY: 0.445 AC XY: 33079 AN XY: 74290

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.396

Alfa AF: 0.398 Hom.: 1583

Bravo AF: 0.456

Asia WGS AF: 0.436 AC: 1520 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	16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1514135; hg19: chr1-56116232;