rs72977016

Positions:

• chr3-140651170-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007096116.1(LOC102724068):​n.265+26569G>A 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 0.021 in 151,606 control chromosomes in the GnomAD database, including 50 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 0.021 (50 hom., cov: 30)
• Consequence: LOC102724068 XR_007096116.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

LOC102724068 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.021 (3185/151606) while in subpopulation NFE AF= 0.0303 (2058/67916). AF 95% confidence interval is 0.0292. There are 50 homozygotes in gnomad4. There are 1512 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 50 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724068	XR_007096116.1	n.265+26569G>A		intron_variant, non_coding_transcript_variant
LOC102724068	XR_001740934.3	n.509+1776G>A		intron_variant, non_coding_transcript_variant
LOC102724068	XR_001740935.3	n.487+1798G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3189 AN: 151488 Hom.: 50 Cov.: 30

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00291

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0303

Gnomad OTH AF: 0.0264

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

GnomAD4 genome AF: 0.0210 AC: 3185 AN: 151606 Hom.: 50 Cov.: 30 AF XY: 0.0204 AC XY: 1512 AN XY: 74030

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0192

Gnomad4 ASJ AF: 0.0162

Gnomad4 EAS AF: 0.000198

Gnomad4 SAS AF: 0.00271

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0303

Gnomad4 OTH AF: 0.0261

Alfa AF: 0.0264 Hom.: 9

Bravo AF: 0.0202

Asia WGS AF: 0.00289 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72977016; hg19: chr3-140370012;