17-70468777-A-G

Position:

• chr17-70468777-A-G

Variant summary

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

The XR_007065977.1(LOC124904100):​n.78+28998A>G 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 0.192 in 152,162 control chromosomes in the GnomAD database, including 3,471 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 0.19 (3471 hom., cov: 32)
• Consequence: LOC124904100 XR_007065977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

Genes affected

LOC124904100 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904100	XR_007065977.1	n.78+28998A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29286 AN: 152042 Hom.: 3470 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.192 AC: 29283 AN: 152162 Hom.: 3471 Cov.: 32 AF XY: 0.196 AC XY: 14616 AN XY: 74388

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.201

Alfa AF: 0.190 Hom.: 366

Bravo AF: 0.212

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717119; hg19: chr17-68464918; COSMIC: COSV50866177;