rs4301693

Variant names:

• chr10-32149271-G-A
• rs4301693
• ENST00000779031.1:n.601G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-32149271-G-A
• chr10-32149271-G-C
• chr10-32149271-G-T

Variant summary

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

The ENST00000779031.1(ENSG00000301470):​n.601G>A 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 0.179 in 152,128 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: ENSG00000301470 ENST00000779031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 5 publications found

Genes affected

ENSG00000301470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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
ENSG00000301470	ENST00000779031.1	n.601G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000301470	ENST00000779033.1	n.294G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301489	ENST00000779267.1	n.152C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000301470	ENST00000779032.1	n.*80G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27232 AN: 152010 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27270 AN: 152128 Hom.: 2640 Cov.: 32 AF XY: 0.181 AC XY: 13493 AN XY: 74368

African (AFR) AF: 0.199 AC: 8256 AN: 41496

American (AMR) AF: 0.166 AC: 2531 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3472

East Asian (EAS) AF: 0.401 AC: 2072 AN: 5170

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4818

European-Finnish (FIN) AF: 0.137 AC: 1446 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10641 AN: 68002

Other (OTH) AF: 0.194 AC: 408 AN: 2104

Alfa AF: 0.157 Hom.: 2130

Bravo AF: 0.184

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs4301693; hg19: chr10-32438199;