3-36350218-T-G

Position:

• chr3-36350218-T-G

Variant summary

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

The XR_007095868.1(LOC124906227):​n.148-14513A>C 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 0.861 in 152,080 control chromosomes in the GnomAD database, including 56,438 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 0.86 (56438 hom., cov: 30)
• Consequence: LOC124906227 XR_007095868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

LOC124906227 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906227	XR_007095868.1	n.148-14513A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130897 AN: 151962 Hom.: 56396 Cov.: 30

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.861 AC: 130997 AN: 152080 Hom.: 56438 Cov.: 30 AF XY: 0.863 AC XY: 64175 AN XY: 74332

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.852

Alfa AF: 0.856 Hom.: 39448

Bravo AF: 0.860

Asia WGS AF: 0.931 AC: 3238 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	2.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1842149; hg19: chr3-36391710;