rs943392

chr9-127963162-G-Achr9-127963162-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001035254.3(EEIG1):c.147-9237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,168 control chromosomes in the GnomAD database, including 31,253 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 0.60 (31253 hom., cov: 33)
• Consequence: EEIG1 NM_001035254.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549

Genes affected

EEIG1 (HGNC:31419): (estrogen-induced osteoclastogenesis regulator 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EEIG1	NM_001035254.3	c.147-9237C>T		intron_variant		ENST00000373095.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEIG1	ENST00000373095.6	c.147-9237C>T		intron_variant		5	NM_001035254.3	P1
EEIG1	ENST00000479828.1	n.24+560C>T		intron_variant, non_coding_transcript_variant		5
EEIG1	ENST00000493175.1	n.88-9558C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91938 AN: 152050 Hom.: 31244 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.604 AC: 91965 AN: 152168 Hom.: 31253 Cov.: 33 AF XY: 0.603 AC XY: 44831 AN XY: 74392

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.611

Alfa AF: 0.690 Hom.: 10165

Bravo AF: 0.587

Asia WGS AF: 0.405 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	5.3
Dann	Benign	0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs943392; hg19: chr9-130725441;