rs1456227

chr3-66954132-C-Achr3-66954132-C-Gchr3-66954132-C-T

Variant summary

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

The XR_940939.2(LOC105377144):n.74+18213G>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 0.766 in 152,038 control chromosomes in the GnomAD database, including 44,939 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 0.77 (44939 hom., cov: 32)
• Consequence: LOC105377144 XR_940939.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

LOC105377144 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377144	XR_940939.2	n.74+18213G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116290 AN: 151920 Hom.: 44896 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.766 AC: 116389 AN: 152038 Hom.: 44939 Cov.: 32 AF XY: 0.769 AC XY: 57153 AN XY: 74306

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.758

Alfa AF: 0.748 Hom.: 5055

Bravo AF: 0.762

Asia WGS AF: 0.889 AC: 3091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456227; hg19: chr3-67004556;