NM_025248.3:c.22+8105C>T

Variant names:

• chr17-38597579-G-A
• rs3892952
• NM_025248.3:c.22+8105C>T

Variant summary

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

The NM_025248.3(SRCIN1):​c.22+8105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,114 control chromosomes in the GnomAD database, including 7,585 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 0.30 (7585 hom., cov: 32)
• Consequence: SRCIN1 NM_025248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 5 publications found

Genes affected

SRCIN1 (HGNC:29506): (SRC kinase signaling inhibitor 1) Enables protein kinase binding activity. Involved in several processes, including regulation of dendritic spine morphogenesis; regulation of protein tyrosine kinase activity; and substrate adhesion-dependent cell spreading. Located in actin cytoskeleton and 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025248.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRCIN1	NM_025248.3	MANE Select	c.22+8105C>T		intron	N/A	NP_079524.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRCIN1	ENST00000617146.5	TSL:1 MANE Select	c.22+8105C>T		intron	N/A	ENSP00000484715.1
	SRCIN1	ENST00000612431.1	TSL:1	c.124+6900C>T		intron	N/A	ENSP00000478342.1
	SRCIN1	ENST00000621492.4	TSL:5	c.22+8105C>T		intron	N/A	ENSP00000483931.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45886 AN: 151996 Hom.: 7571 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.302 AC: 45920 AN: 152114 Hom.: 7585 Cov.: 32 AF XY: 0.307 AC XY: 22848 AN XY: 74354

African (AFR) AF: 0.192 AC: 7984 AN: 41484

American (AMR) AF: 0.443 AC: 6774 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1154 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2776 AN: 5160

South Asian (SAS) AF: 0.359 AC: 1729 AN: 4818

European-Finnish (FIN) AF: 0.277 AC: 2929 AN: 10590

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21432 AN: 67998

Other (OTH) AF: 0.321 AC: 677 AN: 2110

Alfa AF: 0.320 Hom.: 15044

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.062
PhyloP100		-2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3892952; hg19: chr17-36753832;