6-165030331-T-C

Variant names:

• chr6-165030331-T-C
• rs979515
• ENST00000667740.1:n.270-45893T>C

Variant summary

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

The ENST00000667740.1(ENSG00000287877):​n.270-45893T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,014 control chromosomes in the GnomAD database, including 32,372 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 0.65 (32372 hom., cov: 33)
• Consequence: ENSG00000287877 ENST00000667740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

Genes affected

ENSG00000287877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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
ENSG00000287877	ENST00000667740.1	n.270-45893T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98410 AN: 151896 Hom.: 32337 Cov.: 33

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.648 AC: 98503 AN: 152014 Hom.: 32372 Cov.: 33 AF XY: 0.652 AC XY: 48424 AN XY: 74278

African (AFR) AF: 0.716 AC: 29684 AN: 41472

American (AMR) AF: 0.697 AC: 10650 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3470

East Asian (EAS) AF: 0.915 AC: 4712 AN: 5148

South Asian (SAS) AF: 0.647 AC: 3119 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6109 AN: 10542

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40011 AN: 67954

Other (OTH) AF: 0.657 AC: 1389 AN: 2114

Alfa AF: 0.614 Hom.: 90331

Bravo AF: 0.662

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs979515; hg19: chr6-165443820;