chr1-244879010-G-A

Variant names:

• chr1-244879010-G-A
• rs4658673
• XM_047439568.1:c.217-14279C>T

Variant summary

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

The XM_047439568.1(LOC124904588):​c.217-14279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,236 control chromosomes in the GnomAD database, including 2,634 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 0.18 (2634 hom., cov: 30)
• Consequence: LOC124904588 XM_047439568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

Genes affected

LOC124904588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904588	XM_047439568.1	c.217-14279C>T		intron_variant	Intron 2 of 3		XP_047295524.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27382 AN: 151146 Hom.: 2640 Cov.: 30

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.181 AC: 27377 AN: 151236 Hom.: 2634 Cov.: 30 AF XY: 0.184 AC XY: 13562 AN XY: 73802

African (AFR) AF: 0.114 AC: 4700 AN: 41228

American (AMR) AF: 0.193 AC: 2927 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 778 AN: 3464

East Asian (EAS) AF: 0.228 AC: 1172 AN: 5138

South Asian (SAS) AF: 0.191 AC: 914 AN: 4794

European-Finnish (FIN) AF: 0.249 AC: 2566 AN: 10320

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13761 AN: 67824

Other (OTH) AF: 0.162 AC: 340 AN: 2094

Alfa AF: 0.188 Hom.: 8357

Bravo AF: 0.170

Asia WGS AF: 0.170 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4658673; hg19: chr1-245042312;