3-110611435-G-T

Position:

• chr3-110611435-G-T

Variant summary

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

The XR_924328.3(LOC105374037):​n.335+27050C>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 0.155 in 151,988 control chromosomes in the GnomAD database, including 2,766 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 0.16 (2766 hom., cov: 32)
• Consequence: LOC105374037 XR_924328.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

LOC105374037 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374037	XR_924328.3	n.335+27050C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23573 AN: 151872 Hom.: 2753 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0978

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.155 AC: 23620 AN: 151988 Hom.: 2766 Cov.: 32 AF XY: 0.154 AC XY: 11425 AN XY: 74316

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.0978

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0876 Hom.: 1246

Bravo AF: 0.163

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11919628; hg19: chr3-110330282;