chr17-19457898-T-C

Variant names:

• chr17-19457898-T-C
• rs10491097
• ENST00000421796.2:n.282+2805A>G

Variant summary

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

The ENST00000421796.2(ENSG00000235979):​n.282+2805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,088 control chromosomes in the GnomAD database, including 23,159 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 0.49 (23159 hom., cov: 32)
• Consequence: ENSG00000235979 ENST00000421796.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 16 publications found

Genes affected

ENSG00000235979 (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 (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371574	NR_188340.1	n.269+2805A>G		intron_variant	Intron 1 of 1
LOC105371574	NR_188341.1	n.269+2805A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235979	ENST00000421796.2	n.282+2805A>G		intron_variant	Intron 1 of 2	5
ENSG00000231477	ENST00000435953.2	n.239-197T>C		intron_variant	Intron 1 of 1	2
ENSG00000235979	ENST00000456537.7	n.282+2805A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75160 AN: 151970 Hom.: 23163 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.494 AC: 75152 AN: 152088 Hom.: 23159 Cov.: 32 AF XY: 0.486 AC XY: 36116 AN XY: 74344

African (AFR) AF: 0.147 AC: 6080 AN: 41490

American (AMR) AF: 0.499 AC: 7615 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2695 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1039 AN: 5180

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6392 AN: 10576

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47258 AN: 67966

Other (OTH) AF: 0.563 AC: 1187 AN: 2108

Alfa AF: 0.632 Hom.: 41909

Bravo AF: 0.475

Asia WGS AF: 0.276 AC: 961 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	4.4
DANN	Benign	0.65
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs10491097; hg19: chr17-19361211;