rs17161597

chr7-89492356-T-Cchr7-89492356-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655452.1(ENSG00000227863):n.394+646T>C variant causes a intron, non coding transcript 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: ENST00000655452.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375387	XR_927729.3	n.301-37T>C		intron_variant, non_coding_transcript_variant
LOC105375387	XR_927730.3	n.300+646T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655452.1	n.394+646T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0379

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.0498

Gnomad4 SAS AF: 0.0534

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.00247

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.00891 Hom.: 75

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17161597; hg19: chr7-89121670;