17-49901622-C-T

Variant names:

• chr17-49901622-C-T
• rs271674
• ENST00000717207.1:n.449-23C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000717207.1(ENSG00000248954):​n.449-23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,944 control chromosomes in the GnomAD database, including 4,753 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 0.25 (4753 hom., cov: 31)
• Consequence: ENSG00000248954 ENST00000717207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 6 publications found

Genes affected

ENSG00000248954 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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
ENSG00000248954	ENST00000717207.1	n.449-23C>T		intron_variant	Intron 2 of 3
ENSG00000248954	ENST00000746153.1	n.488-23C>T		intron_variant	Intron 2 of 4
ENSG00000248954	ENST00000746154.1	n.815+5510C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37409 AN: 151826 Hom.: 4750 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00887

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.246 AC: 37429 AN: 151944 Hom.: 4753 Cov.: 31 AF XY: 0.242 AC XY: 17967 AN XY: 74280

African (AFR) AF: 0.265 AC: 10980 AN: 41398

American (AMR) AF: 0.234 AC: 3578 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.00909 AC: 47 AN: 5172

South Asian (SAS) AF: 0.236 AC: 1132 AN: 4800

European-Finnish (FIN) AF: 0.210 AC: 2221 AN: 10570

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17931 AN: 67946

Other (OTH) AF: 0.272 AC: 572 AN: 2102

Alfa AF: 0.263 Hom.: 8979

Bravo AF: 0.251

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs271674; hg19: chr17-47978986;