7-89492356-T-C

Variant names:

• chr7-89492356-T-C
• rs17161597
• ENST00000448260.2:n.521+646T>C

Variant summary

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

The ENST00000448260.2(ENSG00000227863):​n.521+646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,230 control chromosomes in the GnomAD database, including 511 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 0.052 (511 hom., cov: 33)
• Consequence: ENSG00000227863 ENST00000448260.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 1 publications found

Genes affected

ENSG00000227863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375387	NR_187912.1	n.872+646T>C		intron_variant	Intron 5 of 6
LOC105375387	NR_187913.1	n.262-37T>C		intron_variant	Intron 3 of 5
LOC105375387	NR_187914.1	n.460-4278T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227863	ENST00000448260.2	n.521+646T>C		intron_variant	Intron 5 of 5	5
ENSG00000227863	ENST00000654764.1	n.226+646T>C		intron_variant	Intron 3 of 4
ENSG00000227863	ENST00000654952.1	n.368+646T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7884 AN: 152112 Hom.: 510 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0380

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0497

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00247

Gnomad OTH AF: 0.0412

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

GnomAD4 genome AF: 0.0519 AC: 7898 AN: 152230 Hom.: 511 Cov.: 33 AF XY: 0.0531 AC XY: 3951 AN XY: 74446

African (AFR) AF: 0.154 AC: 6414 AN: 41524

American (AMR) AF: 0.0379 AC: 579 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3470

East Asian (EAS) AF: 0.0498 AC: 258 AN: 5184

South Asian (SAS) AF: 0.0534 AC: 258 AN: 4830

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00247 AC: 168 AN: 67998

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

Alfa AF: 0.0154 Hom.: 174

Bravo AF: 0.0557

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.32
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs17161597; hg19: chr7-89121670;