rs475032

Variant names:

• chr11-64373265-G-C
• rs475032
• ENST00000757243.1:n.103G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-64373265-G-C
• chr11-64373265-G-T

Variant summary

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

The ENST00000757243.1(ENSG00000298679):​n.103G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,940 control chromosomes in the GnomAD database, including 31,930 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 0.65 (31930 hom., cov: 31)
• Consequence: ENSG00000298679 ENST00000757243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 11 publications found

Genes affected

ENSG00000298679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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
ENSG00000298679	ENST00000757243.1	n.103G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98025 AN: 151822 Hom.: 31907 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.646 AC: 98096 AN: 151940 Hom.: 31930 Cov.: 31 AF XY: 0.644 AC XY: 47822 AN XY: 74264

African (AFR) AF: 0.700 AC: 29017 AN: 41430

American (AMR) AF: 0.623 AC: 9511 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.775 AC: 3984 AN: 5142

South Asian (SAS) AF: 0.615 AC: 2964 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6115 AN: 10564

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42159 AN: 67926

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.526 Hom.: 1567

Bravo AF: 0.653

Asia WGS AF: 0.668 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs475032; hg19: chr11-64140737;