chr1-224223894-G-A

Variant names:

• chr1-224223894-G-A
• rs10799541
• ENST00000420350.1:n.705+66G>A

Variant summary

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

The ENST00000420350.1(ENSG00000237101):​n.705+66G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,000 control chromosomes in the GnomAD database, including 9,373 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 0.35 (9372 hom., cov: 31)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: ENSG00000237101 ENST00000420350.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 8 publications found

Genes affected

ENSG00000237101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420350.1. 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
	LOC101927164	NR_110668.1		n.705+66G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237101	ENST00000420350.1	TSL:1	n.705+66G>A		intron	N/A
	ENSG00000237101	ENST00000734925.1		n.523-3532G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52837 AN: 151876 Hom.: 9371 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.348 AC: 52859 AN: 151994 Hom.: 9372 Cov.: 31 AF XY: 0.351 AC XY: 26057 AN XY: 74282

African (AFR) AF: 0.327 AC: 13560 AN: 41460

American (AMR) AF: 0.412 AC: 6282 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2615 AN: 5170

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4818

European-Finnish (FIN) AF: 0.357 AC: 3770 AN: 10548

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22750 AN: 67960

Other (OTH) AF: 0.356 AC: 749 AN: 2104

Alfa AF: 0.338 Hom.: 37656

Bravo AF: 0.353

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.35
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10799541; hg19: chr1-224411596;