chr6-164902559-A-G

Variant names:

• chr6-164902559-A-G
• rs6455970
• ENST00000837859.1:n.147-1738T>C

Variant summary

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

The ENST00000837859.1(ENSG00000309021):​n.147-1738T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,092 control chromosomes in the GnomAD database, including 6,595 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 0.27 (6595 hom., cov: 32)
• Consequence: ENSG00000309021 ENST00000837859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 1 publications found

Genes affected

ENSG00000309021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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
ENSG00000309021	ENST00000837859.1	n.147-1738T>C		intron_variant	Intron 1 of 3
ENSG00000309021	ENST00000837860.1	n.252-1738T>C		intron_variant	Intron 1 of 3
ENSG00000309021	ENST00000837861.1	n.89-1738T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41182 AN: 151974 Hom.: 6589 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.271 AC: 41223 AN: 152092 Hom.: 6595 Cov.: 32 AF XY: 0.265 AC XY: 19697 AN XY: 74364

African (AFR) AF: 0.439 AC: 18206 AN: 41456

American (AMR) AF: 0.159 AC: 2431 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3470

East Asian (EAS) AF: 0.0986 AC: 510 AN: 5170

South Asian (SAS) AF: 0.152 AC: 733 AN: 4822

European-Finnish (FIN) AF: 0.194 AC: 2051 AN: 10584

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16088 AN: 67984

Other (OTH) AF: 0.230 AC: 485 AN: 2110

Alfa AF: 0.246 Hom.: 13463

Bravo AF: 0.274

Asia WGS AF: 0.171 AC: 596 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	16
DANN	Benign	0.57
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs6455970; hg19: chr6-165316048;