chr1-221865713-C-T

Variant names:

• chr1-221865713-C-T
• rs4240931
• XR_007066885.1:n.330+13648C>T

Variant summary

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

The XR_007066885.1(LOC124904517):​n.330+13648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,988 control chromosomes in the GnomAD database, including 16,202 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 0.46 (16202 hom., cov: 32)
• Consequence: LOC124904517 XR_007066885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

Genes affected

LOC124904517 (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 (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.330+13648C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69354 AN: 151870 Hom.: 16201 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.457 AC: 69385 AN: 151988 Hom.: 16202 Cov.: 32 AF XY: 0.461 AC XY: 34237 AN XY: 74296

Gnomad4 AFR AF: 0.462 AC: 0.46245 AN: 0.46245

Gnomad4 AMR AF: 0.572 AC: 0.571541 AN: 0.571541

Gnomad4 ASJ AF: 0.513 AC: 0.513249 AN: 0.513249

Gnomad4 EAS AF: 0.631 AC: 0.63104 AN: 0.63104

Gnomad4 SAS AF: 0.466 AC: 0.465753 AN: 0.465753

Gnomad4 FIN AF: 0.430 AC: 0.430319 AN: 0.430319

Gnomad4 NFE AF: 0.415 AC: 0.414937 AN: 0.414937

Gnomad4 OTH AF: 0.468 AC: 0.468216 AN: 0.468216

Alfa AF: 0.438 Hom.: 46946

Bravo AF: 0.472

Asia WGS AF: 0.590 AC: 2050 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	1.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4240931; hg19: chr1-222039055;