chr17-42630065-T-G

Variant names:

• chr17-42630065-T-G
• rs2134808
• ENST00000766603.1:n.31-10741A>C

Variant summary

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

The ENST00000766603.1(ENSG00000299802):​n.31-10741A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,188 control chromosomes in the GnomAD database, including 3,245 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 0.18 (3245 hom., cov: 32)
• Consequence: ENSG00000299802 ENST00000766603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 22 publications found

Genes affected

ENSG00000299802 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 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
ENSG00000299802	ENST00000766603.1	n.31-10741A>C		intron_variant	Intron 1 of 3
ENSG00000299802	ENST00000766604.1	n.116+10160A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26882 AN: 152070 Hom.: 3246 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.177 AC: 26871 AN: 152188 Hom.: 3245 Cov.: 32 AF XY: 0.170 AC XY: 12681 AN XY: 74382

African (AFR) AF: 0.0466 AC: 1937 AN: 41546

American (AMR) AF: 0.199 AC: 3038 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1365 AN: 3464

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0747 AC: 360 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1914 AN: 10584

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17346 AN: 67998

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.237 Hom.: 7961

Bravo AF: 0.176

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.64
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2134808; hg19: chr17-40782083;