rs17779747

chr17-70498851-G-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The XR_007065977.1(LOC124904100):n.79-3192G>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.24 in 151,988 control chromosomes in the GnomAD database, including 5,329 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 0.24 (5329 hom., cov: 32)
• Consequence: LOC124904100 XR_007065977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.95

Genes affected

LOC124904100 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904100	XR_007065977.1	n.79-3192G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36393 AN: 151870 Hom.: 5316 Cov.: 32

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.240 AC: 36423 AN: 151988 Hom.: 5329 Cov.: 32 AF XY: 0.235 AC XY: 17498 AN XY: 74304

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.0761

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.275

Alfa AF: 0.313 Hom.: 11461

Bravo AF: 0.232

Asia WGS AF: 0.210 AC: 729 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
Cadd	Benign	19
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17779747; hg19: chr17-68494992;