14-92307319-G-T

Variant summary

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

The XR_944153.1(LOC105370627):n.131+2775G>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 0.318 in 151,860 control chromosomes in the GnomAD database, including 9,639 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.32 (9639 hom., cov: 31)
• Consequence: LOC105370627 XR_944153.1 intron, non_coding_transcript
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.30

Genes affected

LOC105370627 (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 (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370627	XR_944153.1	n.131+2775G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48300 AN: 151740 Hom.: 9635 Cov.: 31

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.318 AC: 48306 AN: 151860 Hom.: 9639 Cov.: 31 AF XY: 0.318 AC XY: 23597 AN XY: 74188

Gnomad4 AFR AF: 0.0834

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.298

Alfa AF: 0.411 Hom.: 28703

Bravo AF: 0.292

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

SKIN/HAIR/EYE PIGMENTATION 6, BLOND/BROWN HAIR Other:1

association, no assertion criteria provided

literature only

OMIM

Oct 06, 2017

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.12
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12896399; hg19: chr14-92773663;