rs834984

chr1-99657782-G-Achr1-99657782-G-Cchr1-99657782-G-T

Variant summary

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

The NM_017734.5(PALMD):c.46-4537G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,942 control chromosomes in the GnomAD database, including 36,818 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 0.69 (36818 hom., cov: 31)
• Consequence: PALMD NM_017734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

PALMD (HGNC:15846): (palmdelphin) Predicted to be involved in regulation of cell shape. Predicted to be located in dendrite. Predicted to be active in cytoplasm. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PALMD	NM_017734.5	c.46-4537G>A		intron_variant		ENST00000263174.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALMD	ENST00000263174.9	c.46-4537G>A		intron_variant		1	NM_017734.5	P1
PALMD	ENST00000605497.5	c.46-4537G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104671 AN: 151824 Hom.: 36764 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.690 AC: 104792 AN: 151942 Hom.: 36818 Cov.: 31 AF XY: 0.690 AC XY: 51234 AN XY: 74254

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.665

Alfa AF: 0.671 Hom.: 6647

Bravo AF: 0.701

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.1
Dann	Benign	0.23

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: rs834984; hg19: chr1-100123338;