1-98115429-A-G

Variant names:

• chr1-98115429-A-G
• rs959707
• ENST00000747811.1:n.126-15985A>G

Variant summary

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

The ENST00000747811.1(ENSG00000297419):​n.126-15985A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,220 control chromosomes in the GnomAD database, including 1,154 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 0.11 (1154 hom., cov: 32)
• Consequence: ENSG00000297419 ENST00000747811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983
• Publications: 1 publications found

Genes affected

ENSG00000297419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900404	XR_007066241.1	n.125+60926A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297419	ENST00000747811.1	n.126-15985A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17027 AN: 152100 Hom.: 1153 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0839

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.112 AC: 17040 AN: 152220 Hom.: 1154 Cov.: 32 AF XY: 0.114 AC XY: 8473 AN XY: 74428

African (AFR) AF: 0.133 AC: 5523 AN: 41544

American (AMR) AF: 0.205 AC: 3134 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 339 AN: 3472

East Asian (EAS) AF: 0.0568 AC: 294 AN: 5176

South Asian (SAS) AF: 0.0711 AC: 343 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1261 AN: 10610

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0839 AC: 5705 AN: 68012

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.0943 Hom.: 457

Bravo AF: 0.123

Asia WGS AF: 0.0800 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.64
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs959707; hg19: chr1-98580985;