rs2764208

Variant names:

• chr6-34746545-A-G
• rs2764208
• ENST00000770922.1:n.319T>C

Variant summary

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

The ENST00000770922.1(ENSG00000300321):​n.319T>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 0.436 in 151,874 control chromosomes in the GnomAD database, including 16,335 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 0.44 (16335 hom., cov: 32)
• Consequence: ENSG00000300321 ENST00000770922.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 27 publications found

Genes affected

ENSG00000300321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300321	ENST00000770922.1	n.319T>C		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000300321	ENST00000770913.1	n.441+9123T>C		intron_variant	Intron 3 of 3
ENSG00000300321	ENST00000770914.1	n.407+9564T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66191 AN: 151762 Hom.: 16289 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.436 AC: 66282 AN: 151874 Hom.: 16335 Cov.: 32 AF XY: 0.435 AC XY: 32316 AN XY: 74238

African (AFR) AF: 0.670 AC: 27671 AN: 41310

American (AMR) AF: 0.355 AC: 5416 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2359 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1531 AN: 4824

European-Finnish (FIN) AF: 0.337 AC: 3568 AN: 10582

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22998 AN: 67966

Other (OTH) AF: 0.449 AC: 945 AN: 2106

Alfa AF: 0.372 Hom.: 8288

Bravo AF: 0.450

Asia WGS AF: 0.364 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2764208; hg19: chr6-34714322;