rs651164

Variant names:

• chr6-160160342-A-G
• rs651164
• ENST00000780339.1:n.440T>C

Variant summary

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

The ENST00000780339.1(ENSG00000301636):​n.440T>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 0.684 in 152,126 control chromosomes in the GnomAD database, including 35,974 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 (35974 hom., cov: 33)
• Consequence: ENSG00000301636 ENST00000780339.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 59 publications found

Genes affected

ENSG00000301636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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
ENSG00000301636	ENST00000780339.1	n.440T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301636	ENST00000780336.1	n.370+1058T>C		intron_variant	Intron 1 of 1
ENSG00000301636	ENST00000780337.1	n.370+1058T>C		intron_variant	Intron 1 of 1
ENSG00000301636	ENST00000780338.1	n.384-57T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 104022 AN: 152008 Hom.: 35935 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.684 AC: 104114 AN: 152126 Hom.: 35974 Cov.: 33 AF XY: 0.678 AC XY: 50445 AN XY: 74376

African (AFR) AF: 0.748 AC: 31048 AN: 41486

American (AMR) AF: 0.635 AC: 9711 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2110 AN: 3466

East Asian (EAS) AF: 0.429 AC: 2221 AN: 5180

South Asian (SAS) AF: 0.574 AC: 2770 AN: 4824

European-Finnish (FIN) AF: 0.671 AC: 7096 AN: 10570

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46851 AN: 67998

Other (OTH) AF: 0.674 AC: 1423 AN: 2110

Alfa AF: 0.681 Hom.: 62476

Bravo AF: 0.686

Asia WGS AF: 0.531 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.86
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs651164; hg19: chr6-160581374; COSMIC: COSV61451926;