3-150116202-G-T

Position:

• chr3-150116202-G-T

Variant summary

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

The NR_136187.1(LOC105374313):​n.156-8736G>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 0.817 in 152,034 control chromosomes in the GnomAD database, including 52,236 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 0.82 (52236 hom., cov: 30)
• Consequence: LOC105374313 NR_136187.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374313	NR_136187.1	n.156-8736G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000487840.5	n.47-8736G>T		intron_variant, non_coding_transcript_variant		2
	ENST00000472821.5	n.156-8736G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000489690.1	n.120-8736G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124163 AN: 151914 Hom.: 52226 Cov.: 30

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.817 AC: 124214 AN: 152034 Hom.: 52236 Cov.: 30 AF XY: 0.818 AC XY: 60799 AN XY: 74332

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.836

Alfa AF: 0.894 Hom.: 8767

Bravo AF: 0.801

Asia WGS AF: 0.685 AC: 2387 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	2.4
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4681577; hg19: chr3-149833989;