6-90314575-G-C

Variant names:

• chr6-90314575-G-C
• rs927297
• ENST00000654016.1:n.44-16789G>C

Variant summary

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

The ENST00000654016.1(ENSG00000260271):​n.44-16789G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,092 control chromosomes in the GnomAD database, including 36,256 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 0.68 (36256 hom., cov: 32)
• Consequence: ENSG00000260271 ENST00000654016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 4 publications found

Genes affected

ENSG00000260271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377891	XR_007059677.1	n.498+16839G>C		intron_variant	Intron 1 of 4
LOC105377891	XR_942778.4	n.499-16789G>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260271	ENST00000654016.1	n.44-16789G>C		intron_variant	Intron 1 of 7
ENSG00000260271	ENST00000663503.1	n.86-16789G>C		intron_variant	Intron 1 of 4
ENSG00000260271	ENST00000667364.1	n.30+19039G>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103993 AN: 151974 Hom.: 36213 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.684 AC: 104079 AN: 152092 Hom.: 36256 Cov.: 32 AF XY: 0.690 AC XY: 51336 AN XY: 74348

African (AFR) AF: 0.771 AC: 31977 AN: 41500

American (AMR) AF: 0.656 AC: 10020 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2187 AN: 3472

East Asian (EAS) AF: 0.978 AC: 5067 AN: 5182

South Asian (SAS) AF: 0.706 AC: 3405 AN: 4820

European-Finnish (FIN) AF: 0.722 AC: 7636 AN: 10578

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41647 AN: 67954

Other (OTH) AF: 0.682 AC: 1435 AN: 2104

Alfa AF: 0.656 Hom.: 4111

Bravo AF: 0.685

Asia WGS AF: 0.790 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.40
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs927297; hg19: chr6-91024294; COSMIC: COSV73888042;