NM_002037.5:c.-18C>A

Variant names:

• chr6-111780572-G-T
• rs12910
• NM_002037.5:c.-18C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002037.5(FYN):​c.-18C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,492 control chromosomes in the GnomAD database, including 27,817 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 0.59 (27774 hom., cov: 32)
  • Exomes 𝑓: 0.45 (43 hom.)
• Consequence: FYN NM_002037.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 15 publications found

Genes affected

FYN (HGNC:4037): (FYN proto-oncogene, Src family tyrosine kinase) This gene is a member of the protein-tyrosine kinase oncogene family. It encodes a membrane-associated tyrosine kinase that has been implicated in the control of cell growth. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the fyn-binding protein. Alternatively spliced transcript variants encoding distinct isoforms exist. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FYN	NM_002037.5	c.-18C>A		5_prime_UTR_variant	Exon 3 of 14	ENST00000354650.7	NP_002028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FYN	ENST00000354650.7	c.-18C>A		5_prime_UTR_variant	Exon 3 of 14	1	NM_002037.5	ENSP00000346671.3

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89579 AN: 151956 Hom.: 27734 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 0.452 AC: 189 AN: 418 Hom.: 43 Cov.: 0 AF XY: 0.448 AC XY: 113 AN XY: 252

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.453 AC: 185 AN: 408

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.590 AC: 89675 AN: 152074 Hom.: 27774 Cov.: 32 AF XY: 0.593 AC XY: 44114 AN XY: 74330

African (AFR) AF: 0.755 AC: 31332 AN: 41500

American (AMR) AF: 0.653 AC: 9976 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4403 AN: 5180

South Asian (SAS) AF: 0.627 AC: 3026 AN: 4826

European-Finnish (FIN) AF: 0.456 AC: 4815 AN: 10556

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32571 AN: 67946

Other (OTH) AF: 0.632 AC: 1331 AN: 2106

Alfa AF: 0.535 Hom.: 13430

Bravo AF: 0.616

Asia WGS AF: 0.699 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	10
DANN	Benign	0.95
PhyloP100		0.17
Mutation Taster		=300/0	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: rs12910; hg19: chr6-112101775; COSMIC: COSV57620950;