10-61900930-G-A

Variant names:

• chr10-61900930-G-A
• rs6415872
• ENST00000827145.1:n.663C>T

Variant summary

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

The ENST00000827145.1(ENSG00000307565):​n.663C>T 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 0.505 in 151,904 control chromosomes in the GnomAD database, including 19,821 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 0.51 (19821 hom., cov: 32)
• Consequence: ENSG00000307565 ENST00000827145.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 5 publications found

Genes affected

ENSG00000307565 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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
ENSG00000307565	ENST00000827145.1	n.663C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000307565	ENST00000827146.1	n.864C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000307565	ENST00000827147.1	n.742C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307586	ENST00000827240.1	n.*100G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76706 AN: 151786 Hom.: 19796 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.505 AC: 76785 AN: 151904 Hom.: 19821 Cov.: 32 AF XY: 0.501 AC XY: 37181 AN XY: 74230

African (AFR) AF: 0.588 AC: 24330 AN: 41408

American (AMR) AF: 0.455 AC: 6951 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1535 AN: 5170

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4824

European-Finnish (FIN) AF: 0.499 AC: 5242 AN: 10504

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33988 AN: 67932

Other (OTH) AF: 0.493 AC: 1039 AN: 2108

Alfa AF: 0.492 Hom.: 24352

Bravo AF: 0.502

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	18
DANN	Benign	0.92
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6415872; hg19: chr10-63660689;