rs2959644

Variant names:

• chr8-98076023-A-G
• rs2959644
• NM_173549.3:c.58+11296A>G

Variant summary

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

The NM_173549.3(ERICH5):​c.58+11296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,152 control chromosomes in the GnomAD database, including 24,328 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 0.56 (24328 hom., cov: 28)
• Consequence: ERICH5 NM_173549.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 4 publications found

Genes affected

ERICH5 (HGNC:26823): (glutamate rich 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERICH5	NM_173549.3	c.58+11296A>G		intron_variant	Intron 1 of 2	ENST00000318528.8	NP_775820.2
ERICH5	NM_001170806.2	c.58+11296A>G		intron_variant	Intron 1 of 1		NP_001164277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERICH5	ENST00000318528.8	c.58+11296A>G		intron_variant	Intron 1 of 2	1	NM_173549.3	ENSP00000315614.3
ERICH5	ENST00000545282.1	c.58+11296A>G		intron_variant	Intron 1 of 1	2		ENSP00000440297.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 84836 AN: 151036 Hom.: 24299 Cov.: 28

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.562 AC: 84911 AN: 151152 Hom.: 24328 Cov.: 28 AF XY: 0.568 AC XY: 41896 AN XY: 73782

African (AFR) AF: 0.452 AC: 18595 AN: 41156

American (AMR) AF: 0.634 AC: 9617 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2077 AN: 3460

East Asian (EAS) AF: 0.690 AC: 3531 AN: 5118

South Asian (SAS) AF: 0.676 AC: 3235 AN: 4786

European-Finnish (FIN) AF: 0.584 AC: 6056 AN: 10376

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 39990 AN: 67786

Other (OTH) AF: 0.557 AC: 1170 AN: 2102

Alfa AF: 0.581 Hom.: 81540

Bravo AF: 0.559

Asia WGS AF: 0.647 AC: 2251 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	1.6
DANN	Benign	0.64
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2959644; hg19: chr8-99088251;