rs3860300

Variant names:

• chr1-206891573-C-G
• rs3860300
• ENST00000830173.1:n.181G>C

Variant summary

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

The ENST00000830173.1(ENSG00000307982):​n.181G>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 0.47 in 152,006 control chromosomes in the GnomAD database, including 17,407 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 0.47 (17407 hom., cov: 32)
• Consequence: ENSG00000307982 ENST00000830173.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 7 publications found

Genes affected

ENSG00000307982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372879	XR_007066835.1	n.238G>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105372879	XR_007066836.1	n.125+4421G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307982	ENST00000830173.1	n.181G>C		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000307982	ENST00000830174.1	n.222G>C		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000307982	ENST00000830172.1	n.177+4056G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71420 AN: 151888 Hom.: 17386 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.470 AC: 71503 AN: 152006 Hom.: 17407 Cov.: 32 AF XY: 0.462 AC XY: 34296 AN XY: 74306

African (AFR) AF: 0.579 AC: 24000 AN: 41434

American (AMR) AF: 0.460 AC: 7025 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1149 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3954 AN: 10550

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31005 AN: 67952

Other (OTH) AF: 0.498 AC: 1052 AN: 2112

Alfa AF: 0.469 Hom.: 2088

Bravo AF: 0.483

Asia WGS AF: 0.277 AC: 965 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	0.62
DANN	Benign	0.72
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3860300; hg19: chr1-207064918;