7-17366094-A-G

Position:

• chr7-17366094-A-G

Variant summary

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

The XR_927074.3(LOC105375171):​n.131-1697T>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 0.248 in 152,100 control chromosomes in the GnomAD database, including 5,439 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 0.25 (5439 hom., cov: 32)
• Consequence: LOC105375171 XR_927074.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC105375171 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375171	XR_927074.3	n.131-1697T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37652 AN: 151982 Hom.: 5424 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.248 AC: 37712 AN: 152100 Hom.: 5439 Cov.: 32 AF XY: 0.246 AC XY: 18288 AN XY: 74352

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.232

Alfa AF: 0.190 Hom.: 3746

Bravo AF: 0.259

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7780687; hg19: chr7-17405718;