rs3904668

chr6-34496233-G-Achr6-34496233-G-Cchr6-34496233-G-T

Variant summary

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

The NM_020804.5(PACSIN1):c.-64+29963G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,080 control chromosomes in the GnomAD database, including 17,398 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 0.46 (17398 hom., cov: 33)
• Consequence: PACSIN1 NM_020804.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

Genes affected

PACSIN1 (HGNC:8570): (protein kinase C and casein kinase substrate in neurons 1) Enables phospholipid binding activity. Involved in plasma membrane tubulation. Located 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PACSIN1	NM_020804.5	c.-64+29963G>A		intron_variant		ENST00000244458.7
PACSIN1	XM_011514541.2	c.-64+11089G>A		intron_variant
PACSIN1	XM_047418689.1	c.-64+11060G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PACSIN1	ENST00000244458.7	c.-64+29963G>A		intron_variant		1	NM_020804.5	P1
PACSIN1	ENST00000374043.6	c.-190+29963G>A		intron_variant		1
PACSIN1	ENST00000620693.4	c.-64+29963G>A		intron_variant		1		P1
PACSIN1	ENST00000493633.5	n.75+11089G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70681 AN: 151960 Hom.: 17386 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.465 AC: 70714 AN: 152080 Hom.: 17398 Cov.: 33 AF XY: 0.467 AC XY: 34709 AN XY: 74342

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.489

Alfa AF: 0.523 Hom.: 42256

Bravo AF: 0.461

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.7
Dann	Benign	0.35

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: rs3904668; hg19: chr6-34464010;