rs736556

Positions:

• chr7-31017453-T-C

Variant summary

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

The XR_001745156.2(LOC105375222):​n.717-8565T>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 0.364 in 152,210 control chromosomes in the GnomAD database, including 16,101 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 0.36 (16101 hom., cov: 33)
• Consequence: LOC105375222 XR_001745156.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

LOC105375222 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375222	XR_001745156.2	n.717-8565T>C		intron_variant, non_coding_transcript_variant
LOC105375222	XR_001745155.2	n.717-8565T>C		intron_variant, non_coding_transcript_variant
LOC105375222	XR_927160.2	n.717-9328T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55278 AN: 152092 Hom.: 16057 Cov.: 33

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.364 AC: 55362 AN: 152210 Hom.: 16101 Cov.: 33 AF XY: 0.356 AC XY: 26513 AN XY: 74432

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.351

Alfa AF: 0.282 Hom.: 1310

Bravo AF: 0.390

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs736556; hg19: chr7-31057068;