1-99677902-A-G

Position:

• chr1-99677902-A-G

Variant summary

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

The NM_017734.5(PALMD):​c.252-8774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,942 control chromosomes in the GnomAD database, including 27,488 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 (27488 hom., cov: 31)
• Consequence: PALMD NM_017734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PALMD	NM_017734.5	c.252-8774A>G		intron_variant		ENST00000263174.9	NP_060204.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALMD	ENST00000263174.9	c.252-8774A>G		intron_variant		1	NM_017734.5	ENSP00000263174	P1
PALMD	ENST00000605497.5	c.252-8774A>G		intron_variant		1		ENSP00000473839

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90965 AN: 151824 Hom.: 27484 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.599 AC: 91008 AN: 151942 Hom.: 27488 Cov.: 31 AF XY: 0.593 AC XY: 44009 AN XY: 74234

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.580

Alfa AF: 0.625 Hom.: 30035

Bravo AF: 0.595

Asia WGS AF: 0.548 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.56

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: rs1981193; hg19: chr1-100143458;