6-85974061-T-C

Variant names:

• chr6-85974061-T-C
• rs806606
• ENST00000666191.1:n.332+6344T>C

Variant summary

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

The ENST00000666191.1(ENSG00000288021):​n.332+6344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 151,972 control chromosomes in the GnomAD database, including 53,599 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 0.84 (53599 hom., cov: 30)
• Consequence: ENSG00000288021 ENST00000666191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 3 publications found

Genes affected

ENSG00000288021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928842	XR_001744239.1	n.1570-19319T>C		intron_variant	Intron 3 of 5
LOC101928842	XR_001744243.1	n.1433-19319T>C		intron_variant	Intron 2 of 4
LOC101928842	XR_002956361.1	n.1992-19319T>C		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288021	ENST00000666191.1	n.332+6344T>C		intron_variant	Intron 3 of 7
ENSG00000288021	ENST00000755500.1	n.264-19319T>C		intron_variant	Intron 1 of 2
ENSG00000288021	ENST00000755501.1	n.110-19319T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127134 AN: 151854 Hom.: 53542 Cov.: 30

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.837 AC: 127252 AN: 151972 Hom.: 53599 Cov.: 30 AF XY: 0.836 AC XY: 62112 AN XY: 74282

African (AFR) AF: 0.935 AC: 38755 AN: 41470

American (AMR) AF: 0.821 AC: 12521 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2697 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4564 AN: 5142

South Asian (SAS) AF: 0.786 AC: 3775 AN: 4802

European-Finnish (FIN) AF: 0.794 AC: 8374 AN: 10552

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53958 AN: 67970

Other (OTH) AF: 0.827 AC: 1746 AN: 2110

Alfa AF: 0.813 Hom.: 101516

Bravo AF: 0.843

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs806606; hg19: chr6-86683779;