rs2050935

Variant names:

• chr1-203362419-C-T
• rs2050935
• ENST00000771305.1:n.148+1235C>T

Variant summary

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

The ENST00000771305.1(ENSG00000300395):​n.148+1235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,114 control chromosomes in the GnomAD database, including 51,178 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 0.82 (51178 hom., cov: 31)
• Consequence: ENSG00000300395 ENST00000771305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 3 publications found

Genes affected

ENSG00000300395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 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
ENSG00000300395	ENST00000771305.1	n.148+1235C>T		intron_variant	Intron 1 of 3
ENSG00000300395	ENST00000771307.1	n.190+1235C>T		intron_variant	Intron 1 of 2
ENSG00000300395	ENST00000771308.1	n.94+1235C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124626 AN: 151996 Hom.: 51128 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.820 AC: 124732 AN: 152114 Hom.: 51178 Cov.: 31 AF XY: 0.821 AC XY: 61046 AN XY: 74372

African (AFR) AF: 0.872 AC: 36172 AN: 41504

American (AMR) AF: 0.849 AC: 12982 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2801 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3700 AN: 5164

South Asian (SAS) AF: 0.804 AC: 3872 AN: 4814

European-Finnish (FIN) AF: 0.809 AC: 8561 AN: 10586

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54011 AN: 67964

Other (OTH) AF: 0.811 AC: 1715 AN: 2114

Alfa AF: 0.803 Hom.: 89179

Bravo AF: 0.825

Asia WGS AF: 0.793 AC: 2754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.35
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2050935; hg19: chr1-203331547;