3-109810703-T-C

Variant names:

• chr3-109810703-T-C
• rs679711
• ENST00000485384.1:n.104T>C

Variant summary

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

The ENST00000485384.1(ENSG00000242029):​n.104T>C 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 0.58 in 151,746 control chromosomes in the GnomAD database, including 25,606 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 0.58 (25602 hom., cov: 30)
  • Exomes 𝑓: 0.72 (4 hom.)
• Consequence: ENSG00000242029 ENST00000485384.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475
• Publications: 4 publications found

Genes affected

ENSG00000242029 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485384.1. 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
	ENSG00000242029	ENST00000485384.1	TSL:2	n.104T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87829 AN: 151610 Hom.: 25554 Cov.: 30

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.560

GnomAD4 exome AF: 0.722 AC: 13 AN: 18 Hom.: 4 Cov.: 0 AF XY: 0.750 AC XY: 9 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.722 AC: 13 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.580 AC: 87941 AN: 151728 Hom.: 25602 Cov.: 30 AF XY: 0.582 AC XY: 43128 AN XY: 74110

African (AFR) AF: 0.619 AC: 25608 AN: 41348

American (AMR) AF: 0.558 AC: 8523 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3472

East Asian (EAS) AF: 0.724 AC: 3709 AN: 5120

South Asian (SAS) AF: 0.673 AC: 3231 AN: 4802

European-Finnish (FIN) AF: 0.495 AC: 5202 AN: 10506

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37698 AN: 67904

Other (OTH) AF: 0.566 AC: 1192 AN: 2106

Alfa AF: 0.565 Hom.: 14671

Bravo AF: 0.585

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.59
PhyloP100		0.47

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: rs679711;

hg19: chr3-109529550;