20-3069244-T-G

Variant names:

• chr20-3069244-T-G
• rs877172
• ENST00000812739.1:n.259A>C

Variant summary

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

The ENST00000812739.1(ENSG00000305741):​n.259A>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 0.361 in 152,080 control chromosomes in the GnomAD database, including 10,241 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 0.36 (10241 hom., cov: 32)
• Consequence: ENSG00000305741 ENST00000812739.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 21 publications found

Genes affected

ENSG00000305741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929098	XR_007067503.1	n.239A>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101929098	XR_430278.4	n.274A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305741	ENST00000812739.1	n.259A>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000305741	ENST00000812740.1	n.470A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54838 AN: 151964 Hom.: 10237 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.361 AC: 54874 AN: 152080 Hom.: 10241 Cov.: 32 AF XY: 0.363 AC XY: 27000 AN XY: 74336

African (AFR) AF: 0.416 AC: 17263 AN: 41460

American (AMR) AF: 0.371 AC: 5673 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2862 AN: 5166

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4818

European-Finnish (FIN) AF: 0.325 AC: 3435 AN: 10580

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 20990 AN: 67982

Other (OTH) AF: 0.422 AC: 894 AN: 2116

Alfa AF: 0.321 Hom.: 14161

Bravo AF: 0.368

Asia WGS AF: 0.422 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.72
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs877172; hg19: chr20-3049890;