chr1-231456224-G-A

Variant names:

• chr1-231456224-G-A
• rs1765811
• ENST00000662216.1:c.30+6214C>T

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+6214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,110 control chromosomes in the GnomAD database, including 9,056 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 0.32 (9056 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 3 publications found

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662216.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287856	ENST00000662216.1		c.30+6214C>T		intron	N/A	ENSP00000499467.1
	ENSG00000287856	ENST00000653908.1		c.30+6214C>T		intron	N/A	ENSP00000499669.1
	ENSG00000287856	ENST00000653198.1		n.433+6248C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48406 AN: 151992 Hom.: 9029 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.319 AC: 48481 AN: 152110 Hom.: 9056 Cov.: 32 AF XY: 0.308 AC XY: 22900 AN XY: 74368

African (AFR) AF: 0.502 AC: 20823 AN: 41460

American (AMR) AF: 0.336 AC: 5136 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3472

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5186

South Asian (SAS) AF: 0.121 AC: 582 AN: 4828

European-Finnish (FIN) AF: 0.183 AC: 1938 AN: 10580

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18080 AN: 67988

Other (OTH) AF: 0.287 AC: 605 AN: 2108

Alfa AF: 0.309 Hom.: 1258

Bravo AF: 0.344

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.9
DANN	Benign	0.85
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1765811; hg19: chr1-231591970;