19-48962703-T-G

Variant names:

• chr19-48962703-T-G
• rs918546
• ENST00000812289.1:n.168T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000812289.1(ENSG00000305667):​n.168T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 148,534 control chromosomes in the GnomAD database, including 13,901 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 0.41 (13901 hom., cov: 24)
• Consequence: ENSG00000305667 ENST00000812289.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 7 publications found

Genes affected

ENSG00000305667 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812289.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305667	ENST00000812289.1		n.168T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000305635	ENST00000812088.1		n.327+2898A>C		intron	N/A
	ENSG00000305635	ENST00000812089.1		n.471+2574A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 61159 AN: 148414 Hom.: 13891 Cov.: 24

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.412 AC: 61182 AN: 148534 Hom.: 13901 Cov.: 24 AF XY: 0.419 AC XY: 30330 AN XY: 72390

African (AFR) AF: 0.204 AC: 8171 AN: 40096

American (AMR) AF: 0.480 AC: 7185 AN: 14978

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1376 AN: 3434

East Asian (EAS) AF: 0.598 AC: 2929 AN: 4896

South Asian (SAS) AF: 0.572 AC: 2640 AN: 4616

European-Finnish (FIN) AF: 0.536 AC: 5464 AN: 10194

Middle Eastern (MID) AF: 0.345 AC: 100 AN: 290

European-Non Finnish (NFE) AF: 0.478 AC: 32065 AN: 67070

Other (OTH) AF: 0.410 AC: 847 AN: 2068

Alfa AF: 0.431 Hom.: 20905

Bravo AF: 0.398

Asia WGS AF: 0.564 AC: 1957 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs918546;

hg19: chr19-49465960;