1-221550182-C-T

Position:

• chr1-221550182-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000419031.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985462	XR_001737823.1	n.225+707C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000419031.2	n.462G>A		non_coding_transcript_exon_variant	1/1
	ENST00000663688.1	n.114+707C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.300

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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.0879

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.241

Alfa AF: 0.247 Hom.: 4768

Bravo AF: 0.214

Asia WGS AF: 0.141 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11118750; hg19: chr1-221723524;