rs1949403

Positions:

• chr3-6053956-C-A
• chr3-6053956-C-G
• chr3-6053956-C-T

Variant summary

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

The ENST00000425894.1(ENSG00000229642):​n.323-70020C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,944 control chromosomes in the GnomAD database, including 36,210 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 0.68 (36210 hom., cov: 31)
• Consequence: ENSG00000229642 ENST00000425894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229642	ENST00000425894.1	n.323-70020C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102836 AN: 151830 Hom.: 36183 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.677 AC: 102908 AN: 151944 Hom.: 36210 Cov.: 31 AF XY: 0.684 AC XY: 50785 AN XY: 74260

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.685

Alfa AF: 0.708 Hom.: 15879

Bravo AF: 0.672

Asia WGS AF: 0.851 AC: 2957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1949403; hg19: chr3-6095643;