rs17166803

Variant names:

• chr7-13150255-C-T
• rs17166803
• ENST00000411542.1:n.112+48672C>T

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.112+48672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 152,162 control chromosomes in the GnomAD database, including 92 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 0.018 (92 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 2 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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
ENSG00000229618	ENST00000411542.1	n.112+48672C>T		intron_variant	Intron 1 of 4	4
ENSG00000229618	ENST00000638964.1	n.485-67290C>T		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.484-67290C>T		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2793 AN: 152044 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00336

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0581

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0183 AC: 2786 AN: 152162 Hom.: 92 Cov.: 32 AF XY: 0.0196 AC XY: 1461 AN XY: 74396

African (AFR) AF: 0.00335 AC: 139 AN: 41536

American (AMR) AF: 0.0182 AC: 278 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3466

East Asian (EAS) AF: 0.165 AC: 847 AN: 5140

South Asian (SAS) AF: 0.0571 AC: 275 AN: 4818

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 960 AN: 68000

Other (OTH) AF: 0.0237 AC: 50 AN: 2114

Alfa AF: 0.0141 Hom.: 6

Bravo AF: 0.0189

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs17166803; hg19: chr7-13189880;