rs72951640

Positions:

• chr3-117524949-C-T

Variant summary

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

The XR_924361.3(LOC105374056):​n.30064-8645C>T 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 0.0452 in 152,264 control chromosomes in the GnomAD database, including 280 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 0.045 (280 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374056	XR_924361.3	n.30064-8645C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6874 AN: 152146 Hom.: 279 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0452 AC: 6881 AN: 152264 Hom.: 280 Cov.: 32 AF XY: 0.0453 AC XY: 3370 AN XY: 74468

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.0437

Gnomad4 FIN AF: 0.0109

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0318 Hom.: 16

Bravo AF: 0.0498

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.33
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72951640; hg19: chr3-117243796;