rs891382

chr4-146231188-G-Achr4-146231188-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REELD1	NM_001354631.1	c.*675G>A		3_prime_UTR_variant	8/8	ENST00000623665.2
REELD1	NM_001371071.1	c.*675G>A		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REELD1	ENST00000623665.2	c.*675G>A		3_prime_UTR_variant	8/8		NM_001354631.1	P1

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

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.737

Alfa AF: 0.706 Hom.: 23525

Bravo AF: 0.770

Asia WGS AF: 0.731 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.11
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs891382; hg19: chr4-147152340;