chr10-6140460-T-G

Variant names:

• chr10-6140460-T-G
• rs3750671
• ENST00000841438.1:n.1213A>C

Variant summary

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

The ENST00000841438.1(ENSG00000309490):​n.1213A>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 0.703 in 152,126 control chromosomes in the GnomAD database, including 37,829 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 0.70 (37829 hom., cov: 32)
• Consequence: ENSG00000309490 ENST00000841438.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.68
• Publications: 9 publications found

Genes affected

ENSG00000309490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928080	XR_930619.3	n.614+558A>C		intron_variant	Intron 1 of 2
LOC101928080	XR_930620.3	n.614+558A>C		intron_variant	Intron 1 of 2
LOC124902369	XR_007062043.1	n.-208T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309490	ENST00000841438.1	n.1213A>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000309490	ENST00000841432.1	n.621+558A>C		intron_variant	Intron 1 of 1
ENSG00000309490	ENST00000841433.1	n.618+558A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106787 AN: 152008 Hom.: 37787 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.703 AC: 106888 AN: 152126 Hom.: 37829 Cov.: 32 AF XY: 0.704 AC XY: 52317 AN XY: 74362

African (AFR) AF: 0.754 AC: 31300 AN: 41510

American (AMR) AF: 0.744 AC: 11370 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2851 AN: 5166

South Asian (SAS) AF: 0.710 AC: 3426 AN: 4822

European-Finnish (FIN) AF: 0.692 AC: 7332 AN: 10592

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45725 AN: 67976

Other (OTH) AF: 0.706 AC: 1491 AN: 2112

Alfa AF: 0.683 Hom.: 109993

Bravo AF: 0.708

Asia WGS AF: 0.657 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0070
DANN	Benign	0.37
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs3750671; hg19: chr10-6182423;