ENST00000419031.2:n.462G>A

Variant names:

• chr1-221550182-C-T
• rs11118750
• ENST00000419031.2:n.462G>A

Variant summary

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

The ENST00000419031.2(ENSG00000227585):​n.462G>A 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 0.208 in 152,334 control chromosomes in the GnomAD database, including 3,518 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 0.21 (3516 hom., cov: 32)
  • Exomes 𝑓: 0.28 (2 hom.)
• Consequence: ENSG00000227585 ENST00000419031.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 3 publications found

Genes affected

ENSG00000227585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419031.2. 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
	ENSG00000227585	ENST00000419031.2	TSL:6	n.462G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000286398	ENST00000775182.1		n.92C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000286398	ENST00000663688.2		n.226+707C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31696 AN: 152120 Hom.: 3515 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.277 AC: 26 AN: 94 Hom.: 2 Cov.: 0 AF XY: 0.308 AC XY: 16 AN XY: 52

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) AF: 0.268 AC: 22 AN: 82

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.208 AC: 31714 AN: 152240 Hom.: 3516 Cov.: 32 AF XY: 0.205 AC XY: 15243 AN XY: 74436

African (AFR) AF: 0.153 AC: 6371 AN: 41556

American (AMR) AF: 0.245 AC: 3742 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3472

East Asian (EAS) AF: 0.0879 AC: 456 AN: 5188

South Asian (SAS) AF: 0.167 AC: 804 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1861 AN: 10586

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16745 AN: 68008

Other (OTH) AF: 0.241 AC: 511 AN: 2116

Alfa AF: 0.244 Hom.: 6062

Bravo AF: 0.214

Asia WGS AF: 0.141 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		2.0

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: rs11118750;

hg19: chr1-221723524;