chr1-100331917-T-C

Position:

• chr1-100331917-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000401024.2(ENSG00000215871):​n.701A>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 0.544 in 1,071,492 control chromosomes in the GnomAD database, including 164,979 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 0.62 (31621 hom., cov: 33)
  • Exomes 𝑓: 0.53 (133358 hom.)
• Consequence: ENST00000401024.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000401024.2	n.701A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94114 AN: 151980 Hom.: 31571 Cov.: 33

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.608

GnomAD4 exome AF: 0.532 AC: 489104 AN: 919394 Hom.: 133358 Cov.: 13 AF XY: 0.532 AC XY: 255008 AN XY: 479120

Gnomad4 AFR exome AF: 0.907

Gnomad4 AMR exome AF: 0.421

Gnomad4 ASJ exome AF: 0.521

Gnomad4 EAS exome AF: 0.454

Gnomad4 SAS exome AF: 0.584

Gnomad4 FIN exome AF: 0.510

Gnomad4 NFE exome AF: 0.525

Gnomad4 OTH exome AF: 0.554

GnomAD4 genome AF: 0.619 AC: 94212 AN: 152098 Hom.: 31621 Cov.: 33 AF XY: 0.617 AC XY: 45825 AN XY: 74326

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.615

Alfa AF: 0.559 Hom.: 6702

Bravo AF: 0.626

Asia WGS AF: 0.573 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs614805; hg19: chr1-100797473;