1-99665088-G-A

Variant names:

• chr1-99665088-G-A
• rs1338571
• NM_017734.5:c.127-2554G>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.127-2554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,724 control chromosomes in the GnomAD database, including 16,078 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 0.45 (16078 hom., cov: 31)
• Consequence: PALMD NM_017734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 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.127-2554G>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.127-2554G>A		intron	N/A	ENSP00000263174.4
	PALMD	ENST00000605497.5	TSL:1	c.127-2554G>A		intron	N/A	ENSP00000473839.1
	ENSG00000301039	ENST00000775735.1		n.389+3535C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 68965 AN: 151606 Hom.: 16076 Cov.: 31

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.455 AC: 68991 AN: 151724 Hom.: 16078 Cov.: 31 AF XY: 0.453 AC XY: 33569 AN XY: 74148

African (AFR) AF: 0.363 AC: 14993 AN: 41354

American (AMR) AF: 0.434 AC: 6610 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1765 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2191 AN: 5164

South Asian (SAS) AF: 0.442 AC: 2130 AN: 4822

European-Finnish (FIN) AF: 0.488 AC: 5137 AN: 10518

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34689 AN: 67850

Other (OTH) AF: 0.436 AC: 919 AN: 2110

Alfa AF: 0.499 Hom.: 14181

Bravo AF: 0.447

Asia WGS AF: 0.407 AC: 1412 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		0.17
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: rs1338571; hg19: chr1-100130644;