1-99690253-T-G

Variant names:

• chr1-99690253-T-G
• rs12071556
• NM_017734.5:c.1612+381T>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.1612+381T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0808 in 152,222 control chromosomes in the GnomAD database, including 1,095 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 0.081 (1095 hom., cov: 32)
• Consequence: PALMD NM_017734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALMD	NM_017734.5	c.1612+381T>G		intron_variant	Intron 7 of 7	ENST00000263174.9	NP_060204.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALMD	ENST00000263174.9	c.1612+381T>G		intron_variant	Intron 7 of 7	1	NM_017734.5	ENSP00000263174.4
PALMD	ENST00000496843.1	n.4771+381T>G		intron_variant	Intron 4 of 4	1
PALMD	ENST00000605497.5	c.*337T>G		downstream_gene_variant		1		ENSP00000473839.1

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12275 AN: 152104 Hom.: 1095 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0808 AC: 12294 AN: 152222 Hom.: 1095 Cov.: 32 AF XY: 0.0780 AC XY: 5805 AN XY: 74438

African (AFR) AF: 0.222 AC: 9221 AN: 41480

American (AMR) AF: 0.0414 AC: 633 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0462 AC: 223 AN: 4828

European-Finnish (FIN) AF: 0.00443 AC: 47 AN: 10616

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0270 AC: 1838 AN: 68026

Other (OTH) AF: 0.0738 AC: 156 AN: 2114

Alfa AF: 0.0243 Hom.: 34

Bravo AF: 0.0896

Asia WGS AF: 0.0360 AC: 127 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		1.2
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: rs12071556; hg19: chr1-100155809;