chr14-30726664-C-T

Variant names:

• chr14-30726664-C-T
• rs10483364
• NM_016106.4:c.1836+4105C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016106.4(SCFD1):​c.1836+4105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0318 in 152,234 control chromosomes in the GnomAD database, including 250 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 0.032 (250 hom., cov: 32)
• Consequence: SCFD1 NM_016106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 2 publications found

Genes affected

SCFD1 (HGNC:20726): (sec1 family domain containing 1) Predicted to enable syntaxin binding activity. Involved in negative regulation of autophagosome assembly; regulation of protein transport; and response to toxic substance. Located in cis-Golgi network. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCFD1	NM_016106.4	c.1836+4105C>T		intron_variant	Intron 23 of 24	ENST00000458591.7	NP_057190.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCFD1	ENST00000458591.7	c.1836+4105C>T		intron_variant	Intron 23 of 24	1	NM_016106.4	ENSP00000390783.2

Frequencies

GnomAD3 genomes AF: 0.0318 AC: 4831 AN: 152116 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.00641

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0318 AC: 4845 AN: 152234 Hom.: 250 Cov.: 32 AF XY: 0.0339 AC XY: 2523 AN XY: 74442

African (AFR) AF: 0.0233 AC: 968 AN: 41538

American (AMR) AF: 0.153 AC: 2335 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 55 AN: 3472

East Asian (EAS) AF: 0.0450 AC: 233 AN: 5180

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4822

European-Finnish (FIN) AF: 0.00641 AC: 68 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0147 AC: 1000 AN: 68010

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0248 Hom.: 457

Bravo AF: 0.0451

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.6
DANN	Benign	0.82
PhyloP100		0.76
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: rs10483364; hg19: chr14-31195870;