chr1-99677902-A-G

Variant names:

• chr1-99677902-A-G
• rs1981193
• NM_017734.5:c.252-8774A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PALMD	NM_017734.5	c.252-8774A>G		intron_variant	Intron 3 of 7	ENST00000263174.9	NP_060204.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALMD	ENST00000263174.9	c.252-8774A>G		intron_variant	Intron 3 of 7	1	NM_017734.5	ENSP00000263174.4
PALMD	ENST00000605497.5	c.252-8774A>G		intron_variant	Intron 3 of 6	1		ENSP00000473839.1

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

African (AFR) AF: 0.563 AC: 23332 AN: 41432

American (AMR) AF: 0.544 AC: 8302 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2238 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2791 AN: 5160

South Asian (SAS) AF: 0.554 AC: 2670 AN: 4816

European-Finnish (FIN) AF: 0.573 AC: 6048 AN: 10554

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43642 AN: 67946

Other (OTH) AF: 0.580 AC: 1226 AN: 2114

Alfa AF: 0.621 Hom.: 38717

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
PhyloP100		-0.13
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: rs1981193; hg19: chr1-100143458;