rs4128691

chr3-72300712-C-T

Variant summary

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

The XR_001740749.3(LOC105377158):n.321+1937G>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 0.295 in 152,108 control chromosomes in the GnomAD database, including 6,848 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 0.29 (6848 hom., cov: 32)
• Consequence: LOC105377158 XR_001740749.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC105377158 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377158	XR_001740749.3	n.321+1937G>A		intron_variant, non_coding_transcript_variant
LOC105377158	XR_001740748.3	n.405+1937G>A		intron_variant, non_coding_transcript_variant
LOC105377158	XR_001740750.3	n.405+1937G>A		intron_variant, non_coding_transcript_variant
LOC105377158	XR_940959.2	n.405+1937G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44785 AN: 151990 Hom.: 6851 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.295 AC: 44804 AN: 152108 Hom.: 6848 Cov.: 32 AF XY: 0.293 AC XY: 21763 AN XY: 74352

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.286

Alfa AF: 0.266 Hom.: 3402

Bravo AF: 0.307

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128691; hg19: chr3-72349863;