1-205707135-T-C

Variant names:

• chr1-205707135-T-C
• rs12748961
• ENST00000767938.1:n.30A>G

Variant summary

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

The ENST00000767938.1(ENSG00000300008):​n.30A>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 0.131 in 152,240 control chromosomes in the GnomAD database, including 2,157 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 0.13 (2157 hom., cov: 32)
• Consequence: ENSG00000300008 ENST00000767938.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 21 publications found

Genes affected

ENSG00000300008 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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
ENSG00000300008	ENST00000767938.1	n.30A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19919 AN: 152122 Hom.: 2146 Cov.: 32

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.131 AC: 19932 AN: 152240 Hom.: 2157 Cov.: 32 AF XY: 0.140 AC XY: 10446 AN XY: 74426

African (AFR) AF: 0.0325 AC: 1352 AN: 41562

American (AMR) AF: 0.150 AC: 2298 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2731 AN: 5176

South Asian (SAS) AF: 0.379 AC: 1822 AN: 4810

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10596

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8903 AN: 68010

Other (OTH) AF: 0.147 AC: 311 AN: 2116

Alfa AF: 0.145 Hom.: 6594

Bravo AF: 0.124

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	16
DANN	Benign	0.72
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12748961; hg19: chr1-205676263;