3-86215133-T-C

Position:

• chr3-86215133-T-C

Variant summary

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

The XR_941024.3(LOC102723364):​n.682+7571A>G 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 0.659 in 151,678 control chromosomes in the GnomAD database, including 33,788 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 0.66 (33788 hom., cov: 32)
• Consequence: LOC102723364 XR_941024.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880

Genes affected

LOC102723364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723364	XR_941024.3	n.682+7571A>G		intron_variant, non_coding_transcript_variant
LOC102723364	XR_427356.5	n.695+7571A>G		intron_variant, non_coding_transcript_variant
LOC102723364	XR_941025.4	n.625+7571A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.660 AC: 99962 AN: 151560 Hom.: 33758 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.659 AC: 100031 AN: 151678 Hom.: 33788 Cov.: 32 AF XY: 0.656 AC XY: 48583 AN XY: 74106

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.655

Alfa AF: 0.713 Hom.: 35542

Bravo AF: 0.643

Asia WGS AF: 0.519 AC: 1782 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2175671; hg19: chr3-86264283;