chr1-99657782-G-A

Variant names:

• chr1-99657782-G-A
• rs834984
• NM_017734.5:c.46-4537G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ENSG00000301039 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017734.5. 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
	PALMD	NM_017734.5	MANE Select	c.46-4537G>A		intron	N/A	NP_060204.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALMD	ENST00000263174.9	TSL:1 MANE Select	c.46-4537G>A		intron	N/A	ENSP00000263174.4
	PALMD	ENST00000605497.5	TSL:1	c.46-4537G>A		intron	N/A	ENSP00000473839.1
	ENSG00000301039	ENST00000775735.1		n.389+10841C>T		intron	N/A

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

African (AFR) AF: 0.825 AC: 34184 AN: 41460

American (AMR) AF: 0.704 AC: 10735 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3470

East Asian (EAS) AF: 0.704 AC: 3628 AN: 5152

South Asian (SAS) AF: 0.618 AC: 2973 AN: 4814

European-Finnish (FIN) AF: 0.633 AC: 6679 AN: 10548

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42191 AN: 67930

Other (OTH) AF: 0.665 AC: 1401 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.23
PhyloP100		0.29
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: rs834984; hg19: chr1-100123338;