4-146231188-G-A

Variant names:

• chr4-146231188-G-A
• rs891382
• NM_001354631.1:c.*675G>A

Variant summary

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

The NM_001354631.1(REELD1):​c.*675G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,122 control chromosomes in the GnomAD database, including 44,252 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 0.75 (44252 hom., cov: 32)
• Consequence: REELD1 NM_001354631.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 6 publications found

Genes affected

REELD1 (HGNC:53638): (reeler domain containing 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001354631.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REELD1	NM_001354631.1	MANE Select	c.*675G>A		3_prime_UTR	Exon 8 of 8	NP_001341560.1
	REELD1	NM_001371071.1		c.*675G>A		3_prime_UTR	Exon 7 of 7	NP_001358000.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REELD1	ENST00000623665.2	TSL:6 MANE Select	c.*675G>A		3_prime_UTR	Exon 8 of 8	ENSP00000510273.1

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114699 AN: 152004 Hom.: 44182 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.755 AC: 114834 AN: 152122 Hom.: 44252 Cov.: 32 AF XY: 0.754 AC XY: 56074 AN XY: 74340

African (AFR) AF: 0.917 AC: 38087 AN: 41536

American (AMR) AF: 0.777 AC: 11874 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3574 AN: 5162

South Asian (SAS) AF: 0.814 AC: 3934 AN: 4830

European-Finnish (FIN) AF: 0.632 AC: 6669 AN: 10548

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46267 AN: 67974

Other (OTH) AF: 0.737 AC: 1556 AN: 2112

Alfa AF: 0.708 Hom.: 34907

Bravo AF: 0.770

Asia WGS AF: 0.731 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.11
DANN	Benign	0.44
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs891382; hg19: chr4-147152340;