chr1-154312576-G-A

Variant names:

• chr1-154312576-G-A
• rs11265530
• ENST00000812093.1:n.975C>T

Variant summary

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

The ENST00000812093.1(ENSG00000305636):​n.975C>T 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 0.28 in 1,597,792 control chromosomes in the GnomAD database, including 65,159 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 0.30 (6915 hom., cov: 30)
  • Exomes 𝑓: 0.28 (58244 hom.)
• Consequence: ENSG00000305636 ENST00000812093.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 8 publications found

Genes affected

ENSG00000305636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 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
ENSG00000305636	ENST00000812093.1	n.975C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000278694	ENST00000612670.1	n.105+10G>A		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.297 AC: 44956 AN: 151500 Hom.: 6908 Cov.: 30

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.279 AC: 402895 AN: 1446174 Hom.: 58244 Cov.: 30 AF XY: 0.282 AC XY: 203010 AN XY: 719846

African (AFR) AF: 0.362 AC: 11880 AN: 32830

American (AMR) AF: 0.302 AC: 13084 AN: 43324

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 4680 AN: 25840

East Asian (EAS) AF: 0.238 AC: 9381 AN: 39446

South Asian (SAS) AF: 0.382 AC: 32628 AN: 85392

European-Finnish (FIN) AF: 0.202 AC: 10508 AN: 51938

Middle Eastern (MID) AF: 0.378 AC: 2150 AN: 5690

European-Non Finnish (NFE) AF: 0.274 AC: 301399 AN: 1101922

Other (OTH) AF: 0.287 AC: 17185 AN: 59792

GnomAD4 genome AF: 0.297 AC: 44983 AN: 151618 Hom.: 6915 Cov.: 30 AF XY: 0.296 AC XY: 21915 AN XY: 74082

African (AFR) AF: 0.361 AC: 14898 AN: 41236

American (AMR) AF: 0.289 AC: 4407 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 622 AN: 3458

East Asian (EAS) AF: 0.251 AC: 1289 AN: 5140

South Asian (SAS) AF: 0.365 AC: 1744 AN: 4782

European-Finnish (FIN) AF: 0.207 AC: 2186 AN: 10548

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18851 AN: 67880

Other (OTH) AF: 0.298 AC: 626 AN: 2104

Alfa AF: 0.290 Hom.: 815

Bravo AF: 0.304

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.76
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs11265530; hg19: chr1-154285052;