6-121890374-T-G

Variant names:

• chr6-121890374-T-G
• rs763075
• ENST00000780095.1:n.54-26970T>G

Variant summary

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

The ENST00000780095.1(ENSG00000289871):​n.54-26970T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,010 control chromosomes in the GnomAD database, including 30,292 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 0.62 (30292 hom., cov: 32)
• Consequence: ENSG00000289871 ENST00000780095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 4 publications found

Genes affected

ENSG00000289871 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377979	XR_001744321.2	n.493+22015T>G		intron_variant	Intron 3 of 6
LOC105377979	XR_001744323.2	n.493+22015T>G		intron_variant	Intron 3 of 6
LOC105377979	XR_001744324.2	n.493+22015T>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289871	ENST00000780095.1	n.54-26970T>G		intron_variant	Intron 1 of 5
ENSG00000289871	ENST00000780096.1	n.135-26970T>G		intron_variant	Intron 1 of 4
ENSG00000289871	ENST00000780097.1	n.438+22015T>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93424 AN: 151892 Hom.: 30247 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.615 AC: 93516 AN: 152010 Hom.: 30292 Cov.: 32 AF XY: 0.609 AC XY: 45244 AN XY: 74280

African (AFR) AF: 0.816 AC: 33867 AN: 41486

American (AMR) AF: 0.461 AC: 7038 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3698 AN: 5160

South Asian (SAS) AF: 0.450 AC: 2163 AN: 4808

European-Finnish (FIN) AF: 0.528 AC: 5562 AN: 10536

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37487 AN: 67964

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.553 Hom.: 39541

Bravo AF: 0.622

Asia WGS AF: 0.586 AC: 2039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs763075; hg19: chr6-122211520; COSMIC: COSV69423950;