chr3-148582691-T-G

Position:

• chr3-148582691-T-G

Variant summary

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

The ENST00000648979.1(ENSG00000285557):​n.110+9127A>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 0.73 in 152,002 control chromosomes in the GnomAD database, including 40,493 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 0.73 (40493 hom., cov: 32)
• Consequence: ENST00000648979.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

Genes affected

(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 (SAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648979.1	n.110+9127A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110898 AN: 151884 Hom.: 40447 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.730 AC: 111002 AN: 152002 Hom.: 40493 Cov.: 32 AF XY: 0.732 AC XY: 54356 AN XY: 74278

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.737

Alfa AF: 0.711 Hom.: 6030

Bravo AF: 0.727

Asia WGS AF: 0.748 AC: 2598 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2639365; hg19: chr3-148300478;