rs3904668

Variant names:

• chr6-34496233-G-A
• rs3904668
• NM_020804.5:c.-64+29963G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-34496233-G-A
• chr6-34496233-G-C
• chr6-34496233-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PACSIN1	NM_020804.5	c.-64+29963G>A		intron_variant	Intron 1 of 9	ENST00000244458.7	NP_065855.1
PACSIN1	XM_011514541.2	c.-64+11089G>A		intron_variant	Intron 1 of 9		XP_011512843.1
PACSIN1	XM_047418689.1	c.-64+11060G>A		intron_variant	Intron 1 of 9		XP_047274645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PACSIN1	ENST00000244458.7	c.-64+29963G>A		intron_variant	Intron 1 of 9	1	NM_020804.5	ENSP00000244458.2
PACSIN1	ENST00000620693.4	c.-64+29963G>A		intron_variant	Intron 1 of 9	1		ENSP00000484060.1
PACSIN1	ENST00000374043.6	c.-190+29963G>A		intron_variant	Intron 1 of 9	1		ENSP00000363155.1
PACSIN1	ENST00000493633.5	n.75+11089G>A		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.303 AC: 12594 AN: 41498

American (AMR) AF: 0.532 AC: 8126 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2257 AN: 3464

East Asian (EAS) AF: 0.317 AC: 1639 AN: 5170

South Asian (SAS) AF: 0.462 AC: 2229 AN: 4826

European-Finnish (FIN) AF: 0.531 AC: 5610 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36423 AN: 67954

Other (OTH) AF: 0.489 AC: 1031 AN: 2108

Alfa AF: 0.511 Hom.: 85554

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
PhyloP100		2.2
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: rs3904668; hg19: chr6-34464010;